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 :  UNDERSTANDING EXTRADIOL DIOXYGENASE MECHANISM IN NAD+ BIOSYNTHESIS BY VIEWING CATALYTIC INTERMEDIATES - 2,3-CIS-4,5-TRANS ACMS BOUND TO I142A MUTANT HAO
 
Authors :  F. Liu, A. Liu
Date :  19 Nov 14  (Deposition) - 10 Feb 16  (Release) - 19 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.84
Chains :  Asym./Biol. Unit :  A
Keywords :  Bi-Cupin Iron-Binding, Dioxygenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Liu, A. Liu
Probing Extradiol Dioxygenase Mechanism In Nad+ Biosynthesi By Viewing Reaction Cycle Intermediates
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 3-HYDROXYANTHRANILATE 3,4-DIOXYGENASE
    Chains: A
    EC Number: 1.13.11.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: NBAC, RMET_5193
    Mutation: YES
    Organism Scientific: RALSTONIA METALLIDURANS
    Organism Taxid: 266264
    Strain: CH34 / ATCC 43123 / DSM 2839
    Synonym: 3-HYDROXYANTHRANILATE OXYGENASE,3-HAO,3-HYDROXYANTHRANILIC ACID DIOXYGENASE,HAD

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
11UC1Ligand/Ion(2E)-2-AMINO-3-[(1E)-3-OXOPROP-1-EN-1-YL]BUT-2-ENEDIOICACID
2FE22Ligand/IonFE (II) ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:51 , GLU A:57 , HIS A:95 , 1UC A:203binding site for residue FE2 A 201
2AC2SOFTWARECYS A:125 , CYS A:128 , CYS A:162 , CYS A:165binding site for residue FE2 A 202
3AC3SOFTWAREARG A:47 , HIS A:51 , GLU A:57 , HIS A:95 , PRO A:97 , ARG A:99 , GLU A:110 , FE2 A:201 , HOH A:342 , HOH A:357 , HOH A:365binding site for residue 1UC A 203

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:23 -Pro A:24
2Gly A:43 -Pro A:44

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4WZC)

(-) 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:174
                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhh.....eee......eeeeee........eee....eeeeeee..eeeeeee..eeeeeee....eeee.....eeee......eeeeeee.......eeeeee......eeeeeee...hhhhhhhhhhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4wzc A   1 MLTYGAPFNFPRWIDEHAHLLKPPVGNRQVWQDSDFIVTVVGGPNHRTDYHDDPLEEFFYQLRGNAYLNLWVDGRRERADLKEGDIFLLPPHVRHSPQRPEAGSACLVIERQRPAGMLDGFEWYCDACGHLVHRVEVQLKSAVTDLPPLFESFYASEDKRRCPHCGQVHPGRAA 174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
   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 4WZC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    1UC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FE2  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:43 - Pro A:44   [ RasMol ]  
    Pro A:23 - Pro A:24   [ 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
  4wzc
    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
  3HAO_CUPMC | Q1LCS4
    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)
  1.13.11.6
    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
  3HAO_CUPMC | Q1LCS4
    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
        3HAO_CUPMC | Q1LCS4: 1yfu 1yfw 1yfx 1yfy 4hsj 4hsl 4hvo 4hvq 4hvr 4i3p 4l2n 4r52

(-) Related Entries Specified in the PDB File

4r52 PRODUCT BOUND FORM OF ENZYME 4R52