Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  BROMIDE SOAKED STRUCTURE OF AN ESTERASE FROM THE OIL-DEGRADING BACTERIUM OLEISPIRA ANTARCTICA
 
Authors :  P. Petit, A. Dong, O. Kagan, A. Savchenko, A. F. Yakunin
Date :  31 May 11  (Deposition) - 15 Jun 11  (Release) - 18 Jul 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Rossmann Fold, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Lemak, A. Tchigvintsev, P. Petit, R. Flick, A. U. Singer, G. Brown, E. Evdokimova, O. Egorova, C. F. Gonzalez, T. N. Chernikova, M. M. Yakimov, M. Kube, R. Reinhardt, P. N. Golyshin, A. Savchenko, A. F. Yakunin
Structure And Activity Of The Cold-Active And Anion-Activated Carboxyl Esterase Olei01171 From The Oil-Degrading Marine Bacterium Oleispira Antarctica.
Biochem. J. V. 445 193 2012
PubMed-ID: 22519667  |  Reference-DOI: 10.1042/BJ20112113

(-) Compounds

Molecule 1 - ESTERASE APC40077
    ChainsA
    EC Number3.1.1.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidP15TV LIC
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneOLEI01171
    Organism ScientificOLEISPIRA ANTARCTICA
    Organism Taxid188908

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1BR1Ligand/IonBROMIDE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:54 , LEU A:55 , SER A:148 , MET A:149 , HOH A:434BINDING SITE FOR RESIDUE BR A 280

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3S8Y)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:112 -Pro A:113

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3S8Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3S8Y)

(-) Exons   (0, 0)

(no "Exon" information available for 3S8Y)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:277
 aligned with D0VWZ4_OLEAN | D0VWZ4 from UniProtKB/TrEMBL  Length:280

    Alignment length:277
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       
         D0VWZ4_OLEAN     3 SIENLSSNKSFGGWHKQYSHVSNTLNCAMRFAIYLPPQASTGAKVPVLYWLSGLTCSDENFMQKAGAQRLAAELGIAIVAPDTSPRGEGVADDEGYDLGQGAGFYVNATQAPWNRHYQMYDYVVNELPELIESMFPVSDKRAIAGHSMGGHGALTIALRNPERYQSVSAFSPINNPVNCPWGQKAFTAYLGKDTDTWREYDASLLMRAAKQYVPALVDQGEADNFLAEQLKPEVLEAAASSNNYPLELRSHEGYDHSYYFIASFIEDHLRFHSNYLN 279
               SCOP domains d3s8ya_ A: automated matches                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------Esterase-3s8yA01 A:23-272                                                                                                                                                                                                                                 ------ Pfam domains
         Sec.struct. author .eeeeeeeee..eeeeeeeeee....eeeeeeeeehhhhhh...eeeeeee.......hhhhhhh.hhhhhhhhh.eeeee..............................hhhhh.hhhhhhhhhhhhhhhhhh.eeeeeeeeeehhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.....eeeeee..........hhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s8y A   2 SIENLSSNKSFGGWHKQYSHVSNTLNCAMRFAIYLPPQASTGAKVPVLYWLSGLTCSDENFMQKAGAQRLAAELGIAIVAPDTSPRGEGVADDEGYDLGQGAGFYVNATQAPWNRHYQMYDYVVNELPELIESMFPVSDKRAIAGHSMGGHGALTIALRNPERYQSVSAFSPINNPVNCPWGQKAFTAYLGKDTDTWREYDASLLMRAAKQYVPALVDQGEADNFLAEQLKPEVLEAAASSNNYPLELRSHEGYDHSYYFIASFIEDHLRFHSNYLN 278
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3S8Y)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (D0VWZ4_OLEAN | D0VWZ4)
molecular function
    GO:0018738    S-formylglutathione hydrolase activity    Catalysis of the reaction: S-formylglutathione + H(2)O = formate + glutathione + H(+).
    GO:0052689    carboxylic ester hydrolase activity    Catalysis of the hydrolysis of a carboxylic ester bond.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
biological process
    GO:0046294    formaldehyde catabolic process    The chemical reactions and pathways resulting in the breakdown of formaldehyde (methanal, H2C=O), the simplest aldehyde.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    BR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:112 - Pro A:113   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3s8y
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  D0VWZ4_OLEAN | D0VWZ4
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  3.1.1.2
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  D0VWZ4_OLEAN | D0VWZ4
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        D0VWZ4_OLEAN | D0VWZ43i6y

(-) Related Entries Specified in the PDB File

3i6y APO-STATE ENZYME