Citations missing date June 2008 Infobox software name PyMOL logo screenshot Image PyMOL large.png 275px caption A PyMOL instance, with the Viewer and GUI visible. developer Schr dinger company Schr dinger, Inc. latest release version 1.4.1 latest release date start date and age 2011 05 02 df yes latest preview version 1.5.0 latest preview date start date and age 2011 10 01 df yes operating system Cross platform genre Molecular modelling license Python license ref http sourceforge.net projects pymol ref website http pymol.org pymol.org PyMOL is an open source, user sponsored, molecular visualization system created by Warren Lyford DeLano and commercialized by DeLano Scientific LLC, which is a private ... using PyMOL. citation needed date September 2010 PyMOL is one of a few open source visualization tools ... . PyMOL rendered protein structures are featured in the 2011 film Contagion film Contagion as part ... for pre compiled PyMOL builds including betas distributed by the company. Access to these executables ... services to obtain access to pre compiled executables. Pre compiled window binaries of PyMOL is also ..., Irvine http www.lfd.uci.edu gohlke pythonlibs pymol here . Acquisition of PyMol by Schr dinger On 8 January 2010, Schr dinger company Schr dinger, Inc. reached an agreement to acquire PyMOL. Schr dinger took over development and maintenance, as well as support and sales of PyMOL, including ... of PyMOL. Gallery gallery Image PyMOL.ogg Example of some molecular editing features of PyMOL, dihedral ... for molecular mechanics modeling References refs External links Commons category Created with PyMol http www.pymol.org PyMOL.org http www.pymolwiki.org index.php Main Page PyMOL Wiki http www.schrodinger.com Schr dinger LLC http www.weizmann.ac.il ISPC eMovie.html Molecular movie making with PyMOL Use dmy dates date February 2011 DEFAULTSORT Pymol Category Molecular modelling software Category Free science software ca PyMOL da PyMOL de PyMOL es PyMOL fr PyMOL ko it PyMOL ja PyMOL zh PyMOL ... more details
Orphan date June 2009 eMovie is a plug in for PyMOL that makes the creation of molecular movies both easy and intuitive via a breakthrough storyboard interface, similar in nature to what is used in the creation of traditional movies. ref The eMovie homepage is accessible at http www.weizmann.ac.il ISPC eMovie.html www.weizmann.ac.il ISPC eMovie.html . ref eMovie is arguably the most user friendly way for users to create movies in PyMOL even inexperienced users . Users interact with a user friendly eMovie GUI that does not require typing commands into PyMOL. Deleted image removed Image eMovie in use.jpg Modular actions such as zooms, rotations, fadings, and morphs morphs require incentive PyMOL can be inserted to any frame in the movie and the actions comprising the movie can be reviewed in list format by viewing the eMovie storyboard. The storyboard also allows for deletion and reinsertion of actions. Movies can be saved, loaded, and exported as a series of image files to be later merged into a traditional movie format such as .mov using an external program like GraphicConverter. eMovie was created at the Israel Structural Proteomics Center ref http www.weizmann.ac.il ISPC home.html Israel Structural Proteomics Center ref ISPC at the Weizmann Institute of Science , and is freely available for download. ref at the http www.weizmann.ac.il ISPC eMovie.html eMovie homepage . ref References reflist Further reading E. Hodis, G. Schreiber, K. Rother and J.L. Sussman 2007 . eMovie a storyboard based tool for making molecular movies . In Trends in Biochemical Sciences 32, 199 204. Category Molecular modelling software Category Data visualization software Category Bioinformatics software Category Free science software deleted license is not specified ... more details
Multiple issues context July 2009 refimprove July 2009 This list of software for protein structure visualization is a compilation of bioinformatics software used to view protein structure s. Such tools are commonly used in molecular biology , and bioinformatics . border 0 align center style border 1px solid 999 background color FFFFFF align left bgcolor CCCCCC NAME Link Author BioBlender http www.bioblender.eu BioBlender official web site SciVis team Visual Molecular Dynamics http www.ks.uiuc.edu Research vmd VMD official website Jmol http www.jmol.org Jmol official web site Jmol development team Geneious Geneious Pro implemented Jmol viewer as part of an all in one sequence analysis software package http www.geneious.com Geneious homepage Geneious development team PyMOL http www.pymolwiki.org index.php Main Page PyMOL Wiki Warren Lyford DeLano RasMol http www.rasmol.org Official website Roger Sayle UCSF Chimera http www.rbvi.ucsf.edu chimera Official website UCSF RBVI STING http www.cbi.cnptia.embrapa.br SMS STAR STING Friend http ilyinlab.org friend Valentin Ilyin http www.molsystems.com vp3ds.html VisProt3DS 3D Stereoscopic view anaglyth, side by side, hardware http www.molsystems.com vp3ds.html Official website Nick Vtyurin http polyview.cchmc.org polyview3d.html Polyview 3D Web based high resolution static views and animations using Pymol or Rasmol http polyview.cchmc.org polyview3d.html Official website Aleksey Porollo & Jarek Meller See also Biological data visualization List of molecular graphics systems List of Open Source Bioinformatics software List of software for molecular mechanics modeling List of nucleic acid simulation software Molecular graphics Category Bioinformatics Category Lists of software Protein Structure Category Bioinformatics software science software stub ... more details
Infobox file format name ccp4 extension tt .ccp4 tt mime owner creatorcode genre electron density file container for contained by extended from extended to The CCP4 file format is file generated by the Collaborative Computational Project Number 4 in 1979. The file format for electron density has become industry standard in X ray crystallography and Cryo electron microscopy where the result of the technique is a three dimensional grid of voxel s each with a value corresponding to density of electrons see wave function The CCP4 format is supported by almost every molecular graphics suite that supports volumetric data. The major packages include Visual molecular dynamics PyMOL UCSF Chimera Bsoft Coot program Coot Chemical Computing Group MOE See also MTZ file format MRC file format EZD file format Chemical file format Protein Data Bank file format Voxel one way of presenting 3D densities External links http www.ccp4.ac.uk html maplib.html description Format technical details Category Computational chemistry Category Chemical file formats chem stub biochem stub ... more details
File 3OJY.png thumb High Resolution Crystal Structure of Human Complement Component 8 protein Name complement component 8, alpha polypeptide caption image width HGNCid 1352 Symbol C8A AltSymbols EntrezGene 731 OMIM 120950 RefSeq NM 000562 UniProt P07357 PDB ECnumber Chromosome 1 Arm p Band 36.2 LocusSupplementaryData 22.1 protein Name complement component 8, beta polypeptide caption image width HGNCid 1353 Symbol C8B AltSymbols EntrezGene 732 OMIM 1209660 RefSeq NM 000066 UniProt P073o58 PDB ECnumber Chromosome 1 Arm p Band 36.2 LocusSupplementaryData 22.1 protein Name complement component 8, gamma polypeptide caption image width HGNCid 1354 Symbol C8G AltSymbols EntrezGene 733 OMIM 120930 RefSeq NM 000606 UniProt P07360 PDB ECnumber Chromosome 9 Arm q Band 34.3 LocusSupplementaryData Complement component 8 is a protein involved in the complement system . A hereditary deficiency of C8 can result in increased susceptibility to Neisseria infections, such as meningitis and gonorrhea. Image Formowanie MAC.svg thumb 400px top Membrane attack complex. Some labels are in Polish. References 1.J Biol Chem. 2011 May 20 286 20 17585 92. Epub 2011 Mar 25. Figure created in Pymol External links MeshName Complement C8 Complement system gene 9 stub Category Complement system The crystal structure is now in the PDB, PDB ID 3OJY. ... more details
File Crystal Structure of Human Diamine Oxidase.png thumb Ribbon representation of human diamine oxidase. ref name pmid19764817 PDB 3HI7 cite journal author McGrath AP, Hilmer KM, Collyer CA, Shepard EM, Elmore BO, Brown DE, Dooley DM, Guss JM title Structure and inhibition of human diamine oxidase journal Biochemistry volume 36 pages 9810 9822 year 2009 pmid 19764817 doi 10.1021 bi9014192 url issn rendered with http pymol.sourceforge.net PyMOL ref protein Name amiloride binding protein 1 amine oxidase copper containing caption image width HGNCid 80 Symbol ABP1 AltSymbols EntrezGene 26 OMIM 104610 RefSeq NM 001091 UniProt P19801 PDB ECnumber 1.4.3.6 Chromosome 7 Arm q Band 34 LocusSupplementaryData qter Amine oxidase is an enzyme involved in the metabolism of histamine . External links MeshName Amine Oxidase Copper Containing CH NH2 oxidoreductases Neurotransmitter metabolism enzymes Histaminergics References references oxidoreductase stub de Diaminoxidase pt Diamina oxidase zh ... more details
File Tonge redo alpha mannosidase.png thumb Cartoon depiction of the Protein Streptococcus pyogenes family GH38 Mannosidase created using PyMol ref cite web title PyMol url http www.pymol.org publisher Schrodinger accessdate 9 14 2011 ref . ref cite journal last Suits first MDL coauthors Yanping Zhu, Edward J. Taylor, Julia Walton, David L. Zechel, Harry J. Gilbert, Gideon J. Davies title Structure and Kinetic Investigation of Streptococcus pyogenes Family GH38 Mannosidase journal Plos One date 3 year 2010 month February volume 5 issue 2 url http www.plosone.org article info 3Adoi 2F10.1371 2Fjournal.pone.0009006 accessdate 9 14 2011 ref lowercase alpha Mannosidase enzyme Name alpha mannosidase EC number 3.2.1.24 CAS number 9025 42 7 IUBMB EC number 3 2 1 24 GO code 0004559 image width caption alpha Mannosidase is an enzyme involved in the cleavage of the alpha form of mannose . Isozymes Humans express the following three alpha mannosidase isozymes protein Name mannosidase, alpha, class 2B, member 1 c aption image width HGNCid 6826 Symbol MAN2B1 AltSymbols MANB EntrezGene 4125 OMIM 609458 RefSeq NM 000528 UniProt O00754 PDB ECnumber 3.2.1.24 Chromosome 19 Arm Band LocusSupplementaryData cen q13.1 protein Name MAN2B2 mannosidase, alpha, class 2B, member 2 caption image width HGNCid 29623 Symbol MAN2B2 AltSymbols KIAA0935 EntrezGene 23324 OMIM RefSeq NM 015274 UniProt Q9Y2E5 PDB ECnumber 3.2.1.24 Chromosome 4 Arm p Band 16.2 LocusSupplementaryData protein Name mannosidase, alpha, class 2C, member 1 caption image width HGNCid 6827 Symbol MAN2C1 AltSymbols MANA1, MANA EntrezGene 4123 OMIM 154580 RefSeq NM 006715 UniProt Q9NTJ4 PDB ECnumber 3.2.1.24 Chromosome 15 Arm q Band 11 LocusSupplementaryData qter Applications It can be utilized in experiments that determine the effects of the presence or absence of mannose on specific molecules, such as recombinant proteins that are used in vaccine development. ref name pmid19520203 cite journal author Vlahopoulos S, Gritzapi ... more details
File MIZ1.png 400px thumb right X ray crystal structure of MIZ1 zinc finger protein http www.rcsb.org pdb explore explore.do?structureId 2Q81 PDB 2Q81 ref cite journal author Stead, M.A., Trinh, C.H., Garnett, J.A., Carr, S.B., Baron, A.J., Edwards, T.A., Wright, S.C. title A beta sheet interaction interface directs the tetramerisation of the Miz 1 POZ domain. journal J.Mol.Biol. volume 373 pages 820 826 year 2007 pmid doi 10.1016 j.jmb.2007.08.026 url issn ref , structure created with PyMol . Infobox protein family Symbol zf MIZ Name zf MIZ image width caption Pfam PF02891 Pfam clan CL0229 InterPro IPR004181 SMART PROSITE MEROPS SCOP TCDB OPM family OPM protein CAZy CDD In molecular biology the MIZ type zinc finger domain is a zinc finger containing protein with Nuclear receptor Family members homology to the Saccharomyces cerevisiae yeast protein, Nfi 1. Miz1 is a sequence specific DNA binding protein that can function as a positive acting transcription genetics transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA binding ability of Msx2. ref name pmid9256341 cite journal author Wu L, Wu H, Ma L, Sangiorgi F, Wu N, Bell JR, Lyons GE, Maxson R title Miz1, a novel zinc finger transcription factor that interacts with Msx2 and enhances its affinity for DNA journal Mech. Dev. volume 65 issue 1 2 pages 3 17 year 1997 month July pmid 9256341 doi 10.1016 S0925 4773 97 00032 4 url ref Other proteins containing this domain include the Homo sapiens human pias family protein Enzyme inhibitor inhibitor of activated STAT protein . The name MIZ is derived from M sx i nteracting z inc finger. The crystal structure of S. cerevisiae sumo e3 ligase siz1 containg this domain has been solved. References reflist InterPro content IPR004181 Category Protein domains ... more details
dablink This page is about CD32 as a biological molecule. For the video game console please see Amiga CD32 . protein Name FCGR2A Fc fragment of IgG, low affinity IIa, receptor CD32 caption image width HGNCid 3616 Symbol FCGR2A AltSymbols FCG2, FCGR2A1, FCGR2 EntrezGene 2212 OMIM 146790 RefSeq NM 021642 UniProt P12318 PDB ECnumber Chromosome 1 Arm q Band 23 LocusSupplementaryData protein Name FCGR2B Fc fragment of IgG, low affinity IIb, receptor CD32 caption Crystal structure of the human fcgamma receptor IIb ectodomain CD32 . ref name pmid10064577 PDB 2FCB cite journal doi 10.1093 emboj 18.5.1095 author Sondermann P, Huber R, Jacob U. title Crystal structure of the soluble form of the human fcgamma receptor IIb a new member of the immunoglobulin superfamily at 1.7 A resolution. journal EMBO J. volume 18 issue 5 pages 1095 103 year 1999 month March pmid 10064577 pmc 1171201 rendered via http pymol.sourceforge.net PyMOL . ref image CD32ray.png width HGNCid 3618 Symbol FCGR2B AltSymbols FCG2, FCGR2 EntrezGene 2213 OMIM 604590 RefSeq NM 004001 UniProt P31994 PDB ECnumber Chromosome 1 Arm q Band 23 LocusSupplementaryData protein Name Fc fragment of IgG, low affinity IIc, receptor for CD32 caption image width HGNCid 15626 Symbol FCGR2C AltSymbols EntrezGene 9103 OMIM RefSeq NM 201563 UniProt P31995 PDB ECnumber Chromosome 1 Arm q Band 23 LocusSupplementaryData CD32 is a surface receptor protein and part of a large population of B cell co receptors, which act to modulate signaling. It has a low affinity for IgG antibodies and down regulates antibody production in the presence of IgG. This feedback loops essentially lowers the production of IgG produced by B cells when there is a surplus in the body. ref Coico, R., Sunshine, G., and Benjamin, E. 2003 . Immunology A Short Course p.97. ref Monoclonal antibodies can distinguish between type A and type B. ref name pmid17386079 cite journal author Veri MC, Gorlatov S, Li H, et al. title Monoclonal antibodies capable of discrimin ... more details
Image HIV genome.png thumb 402px HIV genome Viral infectivity factor , or Vif, is a protein found in HIV and other retrovirus es. Its role is to disrupt the antiviral activity of the human enzyme APOBEC See also APOBEC3G by targeting it for ubiquitination and cellular degradation. APOBEC is a cytidine deaminase enzyme that mutates viral nucleic acids. File Crystal Structure of the HIV Vif BC box in Complex with Human ElonginB and ElonginC.png 400px thumb Ribbon representation of Crystal Structure of the HIV Vif BC box in Complex with Human ElonginB and ElonginC ref cite journal last Stanley first BJ coauthors Ehrlich, E.S., Short, L., Yu, Y., Xiao, Z., Yu, X. F., Xiong, Y. title Structural insight into the human immunodeficiency virus Vif SOCS box and its role in human E3 ubiquitin ligase assembly. journal J.Virol. date 18 year 2008 month Jun volume 82 pages 8656 63 doi 10.1128 JVI.00767 08 pmid 18562529 pmc 2519636 rendered with http pymol.sourceforge.net PyMOL ref Vif is a 23 kilodalton protein that is essential for viral replication. Vif inhibits the cellular protein, APOBEC3G , from entering the virion during budding from a host cell by targeting it for proteasomal degradation. Vif hijacks the cellular Cullin5 E3 ubiquitin ligase, which is composed of ElonginB, ElonginC, Cullin5, and Rbx2, Crystal Structure of the HIV Vif BC box in Complex with Human ElonginB and ElonginC is solved and shown here ref cite journal last Stanley first BJ coauthors Ehrlich, E.S., Short, L., Yu, Y., Xiao, Z., Yu, X. F., Xiong, Y. title Structural insight into the human immunodeficiency virus Vif SOCS box and its role in human E3 ubiquitin ligase assembly. journal J.Virol. date 18 year 2008 month Jun volume 82 pages 8656 63 doi 10.1128 JVI.00767 08 pmid 18562529 pmc 2519636 ref in order to target APOBEC3G for degradation. In the absence of Vif, APOBEC3G causes hypermutation of the viral genome, rendering it dead on arrival at the next host cell. APOBEC3G is thus a host defence to retr ... more details
enzyme Name glucosidase EC number 3.2.1.21 CAS number 9001 22 3 IUBMB EC number 3 2 1 21 GO code 0008422 image Beta glucosidase 3AHX.png width caption The structure of beta glucosidase A from bacterium Clostridium cellulovorans . ref name pmid20682343 PDB 3AHX cite journal author Jeng, W. Y., Wang, N. C., Lin, M. H., Lin, C. T., Liaw, Y. C., Chang, W. J., Liu, C. I., Liang, P. H., Wang, A.H. J. title Structural and functional analysis of three beta glucosidases from bacterium Clostridium cellulovorans, fungus Trichoderma reesei and termite Neotermes koshunensis. journal J.Struc.Biol. year 2010 month August pmid 20682343 doi 10.1016 j.jsb.2010.07.008 url issn volume 173 pages 46 56 issue 1 rendered via http pymol.sourceforge.net PyMOL . ref Beta glucosidase is a glucosidase enzyme that acts upon 1 4 bonds linking two glucose or glucose substituted molecules i.e., the disaccharide cellobiose . It is an exocellulase with specificity for a variety of beta D glycoside substrates. It catalyzes the hydrolysis of terminal non reducing residues in beta D glucosides with release of glucose. ref name isbn1 57259 931 6 cite book author Cox, Michael Lehninger, Albert L Nelson, David R. authorlink editor others title Lehninger principles of biochemistry edition language publisher Worth Publishers location New York year 2000 origyear pages 306 308 quote isbn 1 57259 931 6 oclc doi url accessdate ref Cellulose is largely composed of polymers of beta bond linked glucose molecules, and beta glucosidases are required by organisms some fungi , bacteria , termites that can consume it. These enzymes are a powerful tool for degradation of plant cell walls for pathogens. Lysozyme , an enzyme secreted in tears to prevent bacterial infection of the eye, is also a beta glucosidase that cleaves 1 4 bonds between N acetylglucosamine and N acetylmuramic acid sugars within the peptidoglycan cell walls of gram negative bacteria . NOTOC protein Name GBA3 glucosidase, beta, acid 3 cytosolic capt ... more details
Image 2B9R.png thumb alt Structure of PDB 2B9R human cyclin B rendered with PyMol DeLano Scientific Freeware . Structure of human cyclin B. ref name pmid17495533 cite journal author Petri, E.T., Errico, A., Escobedo, L., Hunt, T., and Basavappa, R. title The crystal structure of human cyclin B journal Cell Cycle volume 11 issue 11 pages 1342 9 year 2007 pmid 17495533 ref protein Name cyclin B1 caption image width HGNCid 1579 Symbol cyclin B1 CCNB1 AltSymbols CCNB EntrezGene 891 OMIM 123836 RefSeq NM 031966 UniProt P14635 PDB ECnumber Chromosome 5 Arm q Band 12 LocusSupplementaryData protein Name cyclin B2 caption image width HGNCid 1580 Symbol cyclin B2 CCNB2 AltSymbols EntrezGene 9133 OMIM 602755 RefSeq NM 004701 UniProt O95067 PDB ECnumber Chromosome 15 Arm q Band 21.3 LocusSupplementaryData protein Name cyclin B3 caption image width HGNCid 18709 Symbol CCNB3 AltSymbols EntrezGene 85417 OMIM 300456 RefSeq NM 033670 UniProt Q8WWL7 PDB ECnumber Chromosome X Arm p Band 11 LocusSupplementaryData Cyclin B is a member of the cyclin family. Cyclin B is a mitosis mitotic cyclin. The amount of cyclin B which binds to Cdk1 and the activity of the cyclin B Cdk complex rise through the cell cycle ref name pmid11089869 cite journal author Ito M title Factors controlling cyclin B expression journal Plant Mol. Biol. volume 43 issue 5 6 pages 677 90 year 2000 month August pmid 11089869 doi 10.1023 A 1006336005587 url http www.kluweronline.com art.pdf?issn 0167 4412&volume 43&page 677 ref until mitosis, where they fall abruptly due to degradation of cyclin B Cdk1 is constitutively present . ref name pmid10582242 cite journal author Hershko A title Mechanisms and regulation of the degradation of cyclin B journal Philos. Trans. R. Soc. Lond., B, Biol. Sci. volume 354 issue 1389 pages 1571 5 discussion 1575 6 year 1999 month September pmid 10582242 pmc 1692665 doi 10.1098 rstb.1999.0500 url ref The complex of Cdk and cyclin B is called maturation promoting factor or mitosis promoting ... more details
image 3HZZ cartoonpic.png thumb upright alt Rendering of Crotonyl CoA Carboxylase Reductase, an oxidoreductase Structure of Crotonyl CoA carboxylase reductase . From Streptomycs collinus . ref name Scarsdale10 PDB 3HZZ cite journal author Scarsdale, J.N., Musayev, F.N., Hazzard, C., Florova, G., Reynolds, K., Wright, H.T. title Structure of Streptomycs collinus crotonyl COA carboxylase reductase journal To be Published year 2010 doi 10.2210 pdb3hzz pdb url http www.rcsb.org pdb explore explore.do?structureId 3HZZ rendered using http pymol.sourceforge.net PyMOL . ref enzyme Name acyl CoA dehydrogenase NADP EC number 1.3.1.8 CAS number 37251 07 3 IUBMB EC number 1 3 1 8 GO code 0047616 image width caption In enzymology , an acyl CoA dehydrogenase NADP EC number 1.3.1.8 is an enzyme that catalysis catalyzes the chemical reaction acyl CoA NADP sup sup math rightleftharpoons math 2,3 dehydroacyl CoA NADPH H sup sup Thus, the two substrate biochemistry substrates of this enzyme are acyl CoA and nicotinamide adenine dinucleotide phosphate NADP sup sup , whereas its 3 product chemistry products are 2,3 dehydroacyl CoA , nicotinamide adenine dinucleotide phosphate NADPH , and hydrogen ion H sup sup . This enzyme belongs to the family of oxidoreductase s, specifically those acting on the CH CH group of donor with NAD or NADP as acceptor. The systematic name of this enzyme class is acyl CoA NADP 2 oxidoreductase . Other names in common use include 2 enoyl CoA reductase , dehydrogenase, acyl coenzyme A nicotinamide adenine dinucleotide , phosphate , enoyl coenzyme A reductase , crotonyl coenzyme A reductase , crotonyl CoA reductase , and acyl CoA dehydrogenase NADP . Structural studies As of late 2007, only one tertiary structure structure has been solved for this class of enzymes, with the Protein Data Bank PDB accession code PDB link 1YXM . References reflist 1 cite journal author Dommes V, Luster W, Cvetanovic M, Kunau WH date 1982 title Purification by affinity chromatograp ... more details
image Apobec.J.Steinfeld.D.png 300px thumb upright alt Colored dice with checkered background Example of a member of the APOBEC family, APOBEC 2 . A cytidine deaminase from Homo Sapiens . ref name Prochnow1 PDB 2NYT cite journal author Prochnow, C., Bransteitter, R., Klein, M.G., Goodman, M.F., Chen, X.S. title The APOBEC 2 crystal structure and functional implications for the deaminase AID. journal Nature volume 445 issue 7126 pages 447 451 year 2007 month pmid 17187054 pmc doi 10.1038 nature05492 url rendered using http pymol.sourceforge.net PyMOL . ref Pfam box Symbol APOBEC N Name APOBEC like N terminal domain image width caption Pfam PF08210 InterPro IPR013158 SMART Prosite SCOP TCDB OPM family OPM protein PDB Pfam box Symbol APOBEC C Name APOBEC like C terminal domain image width caption Pfam PF05240 InterPro IPR007904 SMART Prosite SCOP TCDB OPM family OPM protein PDB APOBEC apolipoprotein B mRNA editing enzyme, catalytic polypeptide like is a family of evolutionary conserved proteins A mechanism of generating protein diversity is messenger RNA mRNA editing. Members of this family are RNA editing C U editing C to U editing enzymes. The N terminus N terminal domain of APOBEC like proteins is the catalytic domain, while the C terminus C terminal domain is a pseudocatalyitc domain. More specifically, the catalytic domain is a zinc dependent cytidine deaminase domain and is essential for cytidine deamination. RNA editing by APOBEC 1 requires homodimerisation and this complex interacts with RNA binding proteins to from the editosome . ref name pmid12683974 cite journal author Wedekind JE, Dance GS, Sowden MP, Smith HC title Messenger RNA editing in mammals new members of the APOBEC family seeking roles in the family business journal Trends Genet. volume 19 issue 4 pages 207 16 year 2003 month April pmid 12683974 doi 10.1016 S0168 9525 03 00054 4 url ref Family members Human genes encoding members of the APOBEC protein family include APOBEC1 APOBEC2 APOBEC3A APOBEC ... more details
Infobox Software name Extensible Computational Chemistry Environment ECCE developer Pacific Northwest National Laboratory latest release version 6.3 latest release date release date 2012 04 4 operating system Linux , Microsoft Windows with a XServer program that supports OpenGL , Mac OS X license EMSL Software User Agreement website URL 1 http ecce.pnl.gov 2 ecce.pnl.gov Extensible Computational Chemistry Environment ECCE The Extensible Computational Chemistry Environment ECCE, pronounced etch provides a sophisticated graphical user interface , scientific visualization tools, and the underlying data management framework enabling scientists to efficiently set up calculations and store, retrieve, and analyze the rapidly growing volumes of data produced by computational chemistry studies. Major features Support for building Molecular modelling molecular models . Graphical user interface to a broad range of electronic structure theory types. Supported codes currently include NWChem , GAMESS UK , Gaussian 03, Gaussian 98, and Amica. Other codes are registered based on user requirements. Graphical user interface for basis set chemistry basis set selection. Remote submission of calculations to UNIX and Linux workstations , Linux Cluster computing clusters , and supercomputers . Supported queue management systems include PBS, LSF, NQE NQS, LoadLeveler and Maui Scheduler. Three dimensional visualization and graphical display of molecular data properties while jobs are running and after completion. Molecular orbital Molecular orbitals and Vibrational frequency vibrational frequencies are among the properties displayed. Support for importing results from NWChem, Gaussian 94, Gaussian 98, and Gaussian 03 calculations run outside of the ECCE environment. Extensive web based help. See also columns list 2 NWChem Molden Avogadro software Gabedit Molekel PyMol Visual Molecular Dynamics VMD Jmol RasMol Ascalaph Designer External links Official http ecce.pnl.gov name ECCE homepage U ... more details
Orphan date March 2011 Pfam box Symbol TarH Name Tar ligand binding domain homologue image width caption Pfam PF02203 InterPro IPR003122 SMART TarH Prosite SCOP 1lih TCDB OPM family OPM protein PDB PDB3 2asr 44 179 PDB3 1wat A 44 179 PDB3 2lig B 44 179 PDB3 1vls 44 179 PDB3 1jmw A 44 179 PDB3 1lih 44 179 PDB3 1was 44 179 File Ligand binding domain aspartate receptor.png thumb right Ribbon diagram of the S. typhimurium aspartate receptor ligand binding domain ref name pmid8831788 PDB 1VLT cite journal author Yeh JI, Biemann HP, Priv GG, Pandit J, Koshland DE Jr, and Kim SH title High resolution structures of the ligand binding domain of the wild type bacterial aspartate receptor journal J Mol Biol volume 262 pages 186 201 year 1996 pmid 8831788 url issn doi 10.1006 jmbi.1996.0507 rendered with http pymol.sourceforge.net PyMOL ref The aspartate receptor , Tar, is a member of a family of cell surface receptor transmembrane receptors that mediate chemotaxis chemotactic response in certain gut flora enteric bacteria , such as Salmonella enterica enterica Salmonella typhimurium and Escherichia coli . ref name PUB00013522 cite journal author Kim SH, Prive GG, Pandit J, Koshland DE, Yeh JI, Biemann HP title High resolution structures of the ligand binding domain of the wild type bacterial aspartate receptor journal J. Mol. Biol. volume 262 issue 2 pages 186 201 year 1996 pmid 8831788 doi 10.1006 jmbi.1996.0507 ref These methyl accepting chemotaxis receptors are one of the first components in the sensory excitation and adaptation responses in bacteria, which act to alter swimming behaviour upon detection of specific chemicals. The aspartate receptor mediates movement towards the attractants aspartic acid aspartate and maltose , and away from the repellents nickel and cobalt. There are many different types of bacterial 60 kDa transmembrane receptors, which share similar topology and signalling mechanisms. They possess three domains a periplasmic ligand binding domain, two tr ... more details
protein name sorbitol dehydrogenase caption Crystallographic structures of sorbitol dehydrogenase. ref name pmid12962626 gallery Image Sorbitol dehydrogenase pymol image.png Helix, Sheet, Loop view Image Sorbitol dehydrogenase pymol image 2.png Molecular view gallery width HGNCid 11184 Symbol SORD AltSymbols EntrezGene 6652 OMIM 182500 RefSeq NM 003104 UniProt Q00796 PDB ECnumber 1.1.1.14 Chromosome 15 Arm q Band 15 LocusSupplementaryData q21.1 Sorbitol dehydrogenase or SDH is a protein . In humans this protein is encoded by the SORD gene . ref name pmid7782086 cite journal author Iwata T, Popescu NC, Zimonjic DB, Karlsson C, H g JO, Vaca G, Rodriguez IR, Carper D title Structural organization of the human sorbitol dehydrogenase gene SORD journal Genomics volume 26 issue 1 pages 55 62 year 1995 month March pmid 7782086 doi 10.1016 0888 7543 95 80082 W url issn ref Sorbitol dehydrogenase is an enzyme in carbohydrate metabolism converting sorbitol , the sugar alcohol form of glucose , into fructose . ref name pmid14965227 cite journal author El Kabbani O, Darmanin C, Chung RP title Sorbitol dehydrogenase structure, function and ligand design journal Curr. Med. Chem. volume 11 issue 4 pages 465 76 year 2004 month February pmid 14965227 doi 10.2174 0929867043455927 url http www.bentham direct.org pages content.php?CMC 2004 00000011 00000004 0008C.SGM issn ref Together with aldose reductase , it provides a way for the body to produce fructose from glucose without using adenosine triphosphate ATP . Sorbitol dehydrogenase uses NAD sup sup as a cofactor its reaction is sorbitol NAD sup sup fructose NADH H sup sup . A zinc ion is also involved in catalysis. Organs that use it most frequently include the liver and seminal vesicle it is found in all kinds of organisms from bacteria to humans . A secondary use is the metabolism of dietary sorbitol , though sorbitol is known not to absorb as well in the intestine as its related compounds glucose and fructose, and is usually fou ... more details
enzyme Name microsomal epoxide hydrolase EC number 3.3.2.9 CAS number 9048 63 9 IUBMB EC number 3 3 2 9 GO code 0033961 image width caption enzyme Name soluble epoxide hydrolase EC number 3.3.2.10 CAS number 9048 63 9 IUBMB EC number 3 3 2 10 GO code 0004301 image Epoxide Hydrolase B 2E3J .png width caption Epoxide hydrolase from Mycobacterium tuberculosis . ref name pmid18585390 PDB 2E3J cite journal author Biswal BK, Morisseau C, Garen G, Cherney MM, Garen C, Niu C, Hammock BD, James MN. title The molecular structure of epoxide hydrolase B from Mycobacterium tuberculosis and its complex with a urea based inhibitor. journal J. Mol. Bio. volume 381 issue 4 pages 897 912 year 2008 month September pmid 18585390 doi 10.1016 j.jmb.2008.06.030 rendered via http pymol.sourceforge.net PyMOL ref Epoxide hydrolase also known as epoxide hydratase functions in detoxication during drug metabolism . It converts epoxide s to trans dihydrodiols, which can be conjugated and excreted from the body. Epoxides result from the degradation of aromatic compound s. Deficiency in this enzyme in patients receiving aromatic type anti epileptic drugs such as phenytoin is reported to lead to DRESS syndrome . Epoxides are significant as cytochrome P450 oxidase metabolites of unsaturated carbon carbon bonds, but are also mutagenic. Epoxide hydrolase is present in large quantity on endoplasmic reticulum . Drug target Mycobacterium tuberculosis, the major causative agent of tuberculosis, expresses at least six different forms of epoxide hydrolase forms A F . The structure of epoxide hydrolase B reveals that the enzyme is a monomer and contains an alpha beta hydrolase fold. In addition to providing insights into the enzyme mechanism, this hydrolase currently serves as a platform for rational drug design of potent inhibitors. In particular, urea based inhibitors have been developed. These inhibitors directly target the catalytic cavity. It is hypothesized that the structure of epoxide hydrolase B may ... more details
infobox biodatabase title ProtCID logo File Database.png description Similar interactions of homologous proteins in multiple crystal forms scope organism center Fox Chase Cancer Center laboratory Institute for Cancer Research author Qifang Xu, Roland Dunbrack pmid Xu & Dunbrack 2011 ref name pmid21036862 released 2010 standard format url http dunbrack2.fccc.edu protcid download webservice sql sparql webapp standalone license versioning frequency curation bookmark version File Activation of ERBB kinases.png thumb Example of cluster of similar interfaces of homologous proteins identified by ProtCID similar homodimers of ERBB kinases EGFR, ERBB2, ERBB4 associated with kinase activation. ref pmid 16777603 ref ref pmid 21454582 ref ref pmid 18334220 ref Each monomer is colored from blue to red from N to C terminus. ProtCID provides PyMol scripts for each cluster to produce similar images. The Protein Common Interface Database ProtCID is a database of similar Protein protein interaction protein protein interfaces in Protein crystallography crystal structures of Sequence homology homologous proteins . ref name pmid21036862 cite journal doi 10.1093 nar gkq1059 title The protein common interface database ProtCID a comprehensive database of interactions of homologous proteins in multiple crystal forms year 2010 last1 Xu first1 Q. last2 Dunbrack first2 R. L. journal Nucleic Acids Research volume 39 pages D761 70 pmid 21036862 issue Database issue pmc 3013667 ref Its main goal is to identify and cluster Protein dimer homodimeric and heterodimeric interfaces observed in multiple crystal forms of homologous proteins. Such interfaces, especially of non identical proteins or protein complexes, have been associated with biologically relevant interactions. ref name pmid18599072 cite journal doi 10.1016 j.jmb.2008.06.002 title Statistical Analysis of Interface Similarity in Crystals of Homologous Proteins year 2008 last1 Xu first1 Qifang last2 Canutescu first2 Adrian A. last3 Wang fir ... more details
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