Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Biol.Unit 2 - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
Image Biol.Unit 2 - manually
Biol.Unit 2 - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF DIVERGENT ENOLASE FROM OCEANOBACILLUS IHEYENSIS COMPLEXED WITH PHOSPHATE
 
Authors :  A. A. Fedorov, E. V. Fedorov, J. M. Sauder, S. K. Burley, J. A. Gerlt, S. C. Almo, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  23 Feb 09  (Deposition) - 03 Mar 09  (Release) - 03 Mar 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  A  (8x)
Keywords :  Structural Genomics, Nysgxrc, Target 9375A, Divergent Enolase, Isomerase, Lyase, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Fedorov, E. V. Fedorov, J. M. Sauder, S. K. Burley, J. A. Gerlt, S. C. Almo
Crystal Structure Of Divergent Enolase From Oceanobacillus Iheyensis Complexed With Phosphate.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MUCONATE CYCLOISOMERASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: OB2843
    Organism Scientific: OCEANOBACILLUS IHEYENSIS HTE831
    Organism Taxid: 221109
    Strain: DSM 14371 / JCM 11309 / KCTC 3954 / HTE831

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A
Biological Unit 2 (8x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1PO42Ligand/IonPHOSPHATE ION
Biological Unit 2 (1, 8)
No.NameCountTypeFull Name
1PO48Ligand/IonPHOSPHATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:89 , TYR A:164 , ASP A:193 , SER A:195 , HIS A:196 , SER A:222 , HIS A:246 , HOH A:501 , HOH A:622BINDING SITE FOR RESIDUE PO4 A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3GD6)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu A:46 -Pro A:47

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GD6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3GD6)

(-) Exons   (0, 0)

(no "Exon" information available for 3GD6)

(-) 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:374
 aligned with GALRD_OCEIH | Q8EMJ9 from UniProtKB/Swiss-Prot  Length:391

    Alignment length:374
                                    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       300       310       320       330       340       350       360       370    
          GALRD_OCEIH     1 MKITDLELHAVGIPRHTGFVNKHVIVKIHTDEGLTGIGEMSDFSHLPLYSVDLHDLKQGLLSILLGQNPFDLMKINKELTDNFPETMYYYEKGSFIRNGIDNALHDLCAKYLDISVSDFLGGRVKEKIKVCYPIFRHRFSEEVESNLDVVRQKLEQGFDVFRLYVGKNLDADEEFLSRVKEEFGSRVRIKSYDFSHLLNWKDAHRAIKRLTKYDLGLEMIESPAPRNDFDGLYQLRLKTDYPISEHVWSFKQQQEMIKKDAIDIFNISPVFIGGLTSAKKAAYAAEVASKDVVLGTTQELSVGTAAMAHLGCSLTNINHTSDPTGPELYVGDVVKNRVTYKDGYLYAPDRSVKGLGIELDESLLAKYQVPDLSW 374
               SCOP domains d3gd6a1 A:1-122 automated matches                                                                                         d3gd6a2 A:123-374 automated matches                                                                                                                                                                                                                          SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee.....eeeeeeeeeee....eeeeee...........hhhhhhhhhhhhhh.....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh......eee..eee......hhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhhhhheeeeee.....hhhhhhhhhhhhh.......eee......hhhhhhhhhhhh...eeee..hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh...........hhhhhh..........ee..eee.............hhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gd6 A   1 MKITDLELHAVGIPRHTGFVNKHVIVKIHTDEGLTGIGEMSDFSHLPLYSVDLHDLKQGLLSILLGQNPFDLMKINKELTDNFPETMYYYEKGSFIRNGIDNALHDLCAKYLDISVSDFLGGRVKEKIKVCYPIFRHRFSEEVESNLDVVRQKLEQGFDVFRLYVGKNLDADEEFLSRVKEEFGSRVRIKSYDFSHLLNWKDAHRAIKRLTKYDLGLEMIESPAPRNDFDGLYQLRLKTDYPISEHVWSFKQQQEMIKKDAIDIFNISPVFIGGLTSAKKAAYAAEVASKDVVLGTTQELSVGTAAMAHLGCSLTNINHTSDPTGPELYVGDVVKNRVTYKDGYLYAPDRSVKGLGIELDESLLAKYQVPDLSW 374
                                    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       300       310       320       330       340       350       360       370
   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  (2, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3GD6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GD6)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (GALRD_OCEIH | Q8EMJ9)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

 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
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu A:46 - Pro A:47   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  3gd6
    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
  GALRD_OCEIH | Q8EMJ9
    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)
  (no 'Enzyme Classificator' available)
    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
  GALRD_OCEIH | Q8EMJ9
    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
        GALRD_OCEIH | Q8EMJ9: 2oqy 3es7 3es8 3fyy 3hpf

(-) Related Entries Specified in the PDB File

2oqy THE SAME PROTEIN IN APO FORM
3es7 THE SAME PROTEIN COMPLEXED WITH MALATE
3es8 THE SAME PROTEIN COMPLEXED WITH MALATE RELATED ID: NYSGXRC-9375A RELATED DB: TARGETDB
3fyy THE SAME PROTEIN IN APO FORM