Structure of PDB 5td3 Chain B Binding Site BS01

Receptor Information

>5td3 Chain B (length=304) Species: 269482 (Burkholderia vietnamiensis G4)

IKVFETREVQDLLKAASSANSTGDARTQQIVLRLLGDLFKAIDDLDITPD
EVWAGVNYLNKLGQDGEAALLAAGLGLEKYLDIRMDAADAALGLDGGTPR
TIEGPLYVAGAPVRDGVAKIDLDADAGAGPLVIHGTVKDLDGKPVAGALV
ECWHANSHGFYSHFDPTGAQRDFNLRGAVRTGADGTYAFRTLMPVGYGCP
PQGATQQLLDRLGRHGNRPAHVHFFVTSDGHRKLTTQFNIEGDPLIWDDF
AYATREELIPPVTTKTGGAALGLKADAYQDITFDFVLTPRVADNQIVERP
RASV

Ligand information

• Ligand ID: ZN
• InChI: InChI=1S/Zn/q+2
• InChIKey: PTFCDOFLOPIGGS-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [Zn++]
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Zn+2]
• Formula: Zn
• Name: ZINC ION
• ChEMBL: CHEMBL1236970
• DrugBank: DB14532
• PDB chain: 5td3 Chain B Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5td3 Crystal structure of Catechol 1,2-dioxygenase from Burkholderia vietnamiensis
• Resolution: 1.75 Å
• Binding residue (original residue number in PDB): Y175 H235 H237
• Binding residue (residue number reindexed from 1): Y161 H221 H223
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): Y175 Y211 R232 H235 H237
• Catalytic site (residue number reindexed from 1): Y161 Y197 R218 H221 H223
• Enzyme Commision number: 1.13.11.1: catechol 1,2-dioxygenase.

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0005506 iron ion binding
• GO:0008199 ferric iron binding
• GO:0016702 oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
• GO:0018576 catechol 1,2-dioxygenase activity
• GO:0046872 metal ion binding
• GO:0051213 dioxygenase activity

Biological Process

• GO:0009712 catechol-containing compound metabolic process
• GO:0019614 catechol-containing compound catabolic process
• GO:0042952 beta-ketoadipate pathway

External links

• PDB: RCSB:5td3, PDBe:5td3, PDBj:5td3
• PDBsum: 5td3
• UniProt: A4JR51