Structure of PDB 1ykk Chain F Binding Site BS01

Receptor Information

>1ykk Chain F (length=238) Species: 303 (Pseudomonas putida)

PAQDNSRFVIRDRNWHPKALTPDYKTSIARSPRQALVSIPQSISETTGPN
FSHLGFGAHDHDLLLNFNNGGLPIGERIIVAGRVVDQYGKPVPNTLVEMW
QANAGGRCRHKNDRYLAPLDPNFGGVGRCLTDSDGYYSFRTIKPGPYPWR
NGPNDWRPAHIHFGISGPSIATKLITQLYFEGDPLIPMCPIVKSIANPEA
VQQLIAKLDMNNANPMDCLAYRFDIVLRGQRKTHFENC

Ligand information

• Ligand ID: FE
• InChI: InChI=1S/Fe/q+3
• InChIKey: VTLYFUHAOXGGBS-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  CACTVS 3.341
  OpenEye OEToolkits 1.5.0: [Fe+3]
• Formula: Fe
• Name: FE (III) ION
• DrugBank: DB13949
• PDB chain: 1ykk Chain F Residue 600

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1ykk Roles of the equatorial tyrosyl iron ligand of protocatechuate 3,4-dioxygenase in catalysis
• Resolution: 2.06 Å
• Binding residue (original residue number in PDB): Y447 H460 H462
• Binding residue (residue number reindexed from 1): Y147 H160 H162
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): C408 Y447 R457 H460 H462
• Catalytic site (residue number reindexed from 1): C108 Y147 R157 H160 H162
• Enzyme Commision number: 1.13.11.3: protocatechuate 3,4-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:0018578 protocatechuate 3,4-dioxygenase activity
• GO:0046872 metal ion binding
• GO:0051213 dioxygenase activity

Biological Process

• GO:0009056 catabolic process
• GO:0019619 3,4-dihydroxybenzoate catabolic process
• GO:0042952 beta-ketoadipate pathway

External links

• PDB: RCSB:1ykk, PDBe:1ykk, PDBj:1ykk
• PDBsum: 1ykk
• PubMed: 16101286
• UniProt: P00437|PCXB_PSEPU Protocatechuate 3,4-dioxygenase beta chain (Gene Name=pcaH)