Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)

(-) Description

Title :  REACTION PRODUCT OF PARAOXON AND S-FORMYLGLUTATHIONE HYDROLASE W197I MUTANT
 
Authors :  P. M. Legler, C. B. Millard
Date :  04 Feb 08  (Deposition) - 12 Aug 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.17
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Cysteine Sulfenic Acid, Serine Hydrolase, Thioesterase, Formaldehyde, Organophosphate, Cytoplasm, Serine Esterase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. M. Legler, D. Kumaran, S. Swaminathan, F. W. Studier, C. B. Millard
Structural Characterization And Reversal Of The Natural Organophosphate Resistance Of A D-Type Esterase, Saccharomyces Cerevisiae S-Formylglutathione Hydrolase.
Biochemistry V. 47 9592 2008
PubMed-ID: 18707125  |  Reference-DOI: 10.1021/BI8010016
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - S-FORMYLGLUTATHIONE HYDROLASE
    Chains: A
    EC Number: 3.1.2.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET13
    Expression System Strain: BL-21(DE3)
    Expression System Vector Type: PLASMID
    Gene: YJL068C
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Synonym: FGH

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1CSO1Mod. Amino AcidS-HYDROXYCYSTEINE
2SDP1Mod. Amino Acid2-AMINO-3-(DIETHOXY-PHOSPHORYLOXY)-PROPIONIC ACID
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1CSO2Mod. Amino AcidS-HYDROXYCYSTEINE
2SDP2Mod. Amino Acid2-AMINO-3-(DIETHOXY-PHOSPHORYLOXY)-PROPIONIC ACID

(-) Sites  (0, 0)

(no "Site" information available for 3C6B)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3C6B)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu A:117 -Pro A:118

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3C6B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3C6B)

(-) Exons   (1, 1)

Asymmetric Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YJL068C1YJL068C.1X:313909-313010900SFGH_YEAST1-2992991A:1-299 (gaps)299

(-) Sequences/Alignments

Asymmetric 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:291
 aligned with SFGH_YEAST | P40363 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:299
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290         
           SFGH_YEAST     1 MKVVKEFSVCGGRLIKLSHNSNSTKTSMNVNIYLPKHYYAQDFPRNKRIPTVFYLSGLTCTPDNASEKAFWQFQADKYGFAIVFPDTSPRGDEVANDPEGSWDFGQGAGFYLNATQEPYAQHYQMYDYIHKELPQTLDSHFNKNGDVKLDFLDNVAITGHSMGGYGAICGYLKGYSGKRYKSCSAFAPIVNPSNVPWGQKAFKGYLGEEKAQWEAYDPCLLIKNIRHVGDDRILIHVGDSDPFLEEHLKPELLLEAVKATSWQDYVEIKKVHGFDHSYYFVSTFVPEHAEFHARNLGLI 299
               SCOP domains d3c6ba_ A: automated matches                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 3c6bA00 A:1-299  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..eeeeeeeee......eeeeeeeehhhhhh........eeeeeee......hhhhhhhhhhhhhhhhhh.eeee.................................hhhhh.hhhhhhhhhhhhhhhhhhh-----.eeeeeeeeeee.hhhhhhhhhhhhhh.......eeeee....hhhhhhhhhhhhhhhhh---..hhhhhhhhhhhhh.......eeeeee...........hhhhhhhh....hhh.eeeeee.....hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-299 (gaps) UniProt: 1-299                                                                                                                                                                                                                                                                Transcript 1
                 3c6b A   1 MKVVKEFSVCGGRLIKLSHNSNSTKTSMNVNIYLPKHYYAQDFPRNKRIPTVFYLSGLTcTPDNASEKAFWQFQADKYGFAIVFPDTSPRGDEVANDPEGSWDFGQGAGFYLNATQEPYAQHYQMYDYIHKELPQTLDSHFN-----KLDFLDNVAITGHsMGGYGAICGYLKGYSGKRYKSCSAFAPIVNPSNVPIGQKAFKGYLG---AQWEAYDPCLLIKNIRHVGDDRILIHVGDSDPFLEEHLKPELLLEAVKATSWQDYVEIKKVHGFDHSYYFVSTFVPEHAEFHARNLGLI 299
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140 |     150       160|      170       180       190       200      |  -|      220       230       240       250       260       270       280       290         
                                                                                      60-CSO                                                                           142   148          161-SDP                                       207 211
   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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3C6B)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (SFGH_YEAST | P40363)
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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

 Visualization

(-) Interactive Views

Asymmetric 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
    CSO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SDP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 3c6b)
 
  Cis Peptide Bonds
    Glu A:117 - Pro A:118   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3c6b
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  SFGH_YEAST | P40363
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.1.2.12
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  SFGH_YEAST | P40363
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SFGH_YEAST | P40363: 1pv1 4flm 4fol

(-) Related Entries Specified in the PDB File

1pv1 S. CEREVISAE S-FORMYLGLUTATHIONE HYDROLASE