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 :  CRYSTAL STRUCTURE OF CG1458 WITH INHIBITOR
 
Authors :  T. T. Ran, W. W. Wang, D. Q. Xu, Y. Y. Gao
Date :  15 Jan 12  (Deposition) - 28 Nov 12  (Release) - 28 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxaloacetate Decarboxylase, Oxalate, Mg++, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Ran, Y. Gao, M. Marsh, W. Zhu, M. Wang, X. Mao, L. Xu, D. Xu, W. Wang
Crystal Structures Of Cg1458 Reveal A Catalytic Lid Domain And A Common Catalytic Mechanism For Fah Family.
Biochem. J. V. 449 51 2013
PubMed-ID: 23046410  |  Reference-DOI: 10.1042/BJ20120913

(-) Compounds

Molecule 1 - 2-HYDROXYHEPTA-2,4-DIENE-1,7-DIOATE ISOMERASE
    Chains: A, B
    EC Number: 5.3.3.-, 4.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: CORYNEBACTERIUM GLUTAMICUM
    Organism Taxid: 1718
    Synonym: 2-KETO-4-PENTENOATE HYDRATASE/2-OXOHEPTA-3-ENE-1,7-DIOIC ACID HYDRATASE (CATECHOL PATHWAY)

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1MG3Ligand/IonMAGNESIUM ION
2OXL2Ligand/IonOXALATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:116 , GLU A:118 , ASP A:147 , LYS A:164 , OXL A:402 , HOH A:501BINDING SITE FOR RESIDUE MG A 401
2AC2SOFTWAREGLY A:67 , ARG A:68 , HIS A:73 , PHE A:90 , GLU A:116 , GLU A:118 , ASP A:147 , LYS A:164 , GLY A:237 , SER A:238 , MG A:401 , HOH A:501 , HOH A:502 , HOH A:503 , HOH A:504BINDING SITE FOR RESIDUE OXL A 402
3AC3SOFTWAREGLU B:116 , GLU B:118 , ASP B:147 , OXL B:402 , HOH B:501BINDING SITE FOR RESIDUE MG B 401
4AC4SOFTWAREGLY B:67 , ARG B:68 , HIS B:73 , PHE B:90 , GLU B:116 , GLU B:118 , ASP B:147 , LYS B:164 , SER B:238 , MG B:401 , HOH B:502 , HOH B:503 , HOH B:504BINDING SITE FOR RESIDUE OXL B 402
5AC5SOFTWAREHOH B:518 , HOH B:575 , HOH B:576 , HOH B:577 , HOH B:578 , HOH B:579BINDING SITE FOR RESIDUE MG B 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4DBH)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:173 -Pro A:174
2Gly B:173 -Pro B:174

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DBH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4DBH)

(-) Exons   (0, 0)

(no "Exon" information available for 4DBH)

(-) 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:269
 aligned with Q8NQY2_CORGL | Q8NQY2 from UniProtKB/TrEMBL  Length:268

    Alignment length:269
                             1                                                                                                                                                                                                                                                                           
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259         
         Q8NQY2_CORGL     - -MRFGRIATPDGMCFCSIEGEGDDVANLTAREIEGTPFTEPKFTGREWPLKDVRLLAPMLPSKVVAIGRNYADHVAEVFKKSAESLPPTLFLKPPTAVTGPESPIRIPSFATKVEFEGELAVVIGKPCKNVKADDWKSVVLGFTIINDVSSRDLQFADGQWARAKGIDTFGPIGPWIETDINSIDLDNLPIKARLTHDGETQLKQDSNSNQMIMKMGEIIEFITASMTLLPGDVIATGSPAGTEAMVDGDYIEIEIPGIGKLGNPVVDA 268
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eeeeeeee...hhh.eeeeee.........eeeeeee.hhheee.......eeeee..hhhhhhhhhh.hhhhh..eeeeehhh.ee.....eee......ee..eeeeeee.......hhhhhhh.eeeeeeee..eehhhhhhhh.hhhhhhh...eeeeeeee.hhhhh.....eeeeeeee..eeeeeeeee.hhh..hhhhhhhhhhhhh......eee..............eeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dbh A   0 HMRFGRIATPDGMCFCSIEGEGDDVANLTAREIEGTPFTEPKFTGREWPLKDVRLLAPMLPSKVVAIGRNYADHVAEVFKKSAESLPPTLFLKPPTAVTGPESPIRIPSFATKVEFEGELAVVIGKPCKNVKADDWKSVVLGFTIINDVSSRDLQFADGQWARAKGIDTFGPIGPWIETDINSIDLDNLPIKARLTHDGETQLKQDSNSNQMIMKMGEIIEFITASMTLLPGDVIATGSPAGTEAMVDGDYIEIEIPGIGKLGNPVVDA 268
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259         


Chain B from PDB  Type:PROTEIN  Length:269
 aligned with Q8NQY2_CORGL | Q8NQY2 from UniProtKB/TrEMBL  Length:268

    Alignment length:269
                             1                                                                                                                                                                                                                                                                           
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259         
         Q8NQY2_CORGL     - -MRFGRIATPDGMCFCSIEGEGDDVANLTAREIEGTPFTEPKFTGREWPLKDVRLLAPMLPSKVVAIGRNYADHVAEVFKKSAESLPPTLFLKPPTAVTGPESPIRIPSFATKVEFEGELAVVIGKPCKNVKADDWKSVVLGFTIINDVSSRDLQFADGQWARAKGIDTFGPIGPWIETDINSIDLDNLPIKARLTHDGETQLKQDSNSNQMIMKMGEIIEFITASMTLLPGDVIATGSPAGTEAMVDGDYIEIEIPGIGKLGNPVVDA 268
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eeeeeeee...hhh.eeeeee.........eeeeeee.hhhee........eeeee..hhhhhhhhhh.hhhhh..eeeeehhh.ee.....eee......ee..eeeeeee.......hhhhhhh.eeeeeeee..eehhhhhhhh.hhhhhhh...eeeeeeee.hhhhh.....eeeeeeee..eeeeeeeee.hhh..hhhhhhhhhhh........eee..............eeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dbh B   0 HMRFGRIATPDGMCFCSIEGEGDDVANLTAREIEGTPFTEPKFTGREWPLKDVRLLAPMLPSKVVAIGRNYADHVAEVFKKSAESLPPTLFLKPPTAVTGPESPIRIPSFATKVEFEGELAVVIGKPCKNVKADDWKSVVLGFTIINDVSSRDLQFADGQWARAKGIDTFGPIGPWIETDINSIDLDNLPIKARLTHDGETQLKQDSNSNQMIMKMGEIIEFITASMTLLPGDVIATGSPAGTEAMVDGDYIEIEIPGIGKLGNPVVDA 268
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259
   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  (0, 0)

(no "SCOP Domain" information available for 4DBH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4DBH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DBH)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8NQY2_CORGL | Q8NQY2)
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:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    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/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
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    OXL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:173 - Pro A:174   [ RasMol ]  
    Gly B:173 - Pro B:174   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  4dbh
    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
  Q8NQY2_CORGL | Q8NQY2
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  4.1.1.-
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  5.3.3.-
    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
  Q8NQY2_CORGL | Q8NQY2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8NQY2_CORGL | Q8NQY2: 4dbf

(-) Related Entries Specified in the PDB File

4dbf THE SAME PROTEIN WITHOUT INHIBITOR