Structure of PDB 2gbx Chain C Binding Site BS03

Receptor Information

>2gbx Chain C (length=446) Species: 13690 (Sphingobium yanoikuyae)

TLVDTVNASQSRQVFWDEDVYALEIERIFSRAWLMLGHESLVPKPGDFIT
TYMAEDKVILSHQSDGTFRAFINSCSHRGNQICHADSGNAKAFVCNYHGW
VFGQDGSLVDVPLESRCYHNSLDKQKLAAKSVRVETYKGFIFGCHDPEAP
SLEDYLGEFRYYLDTIWEGAGGGMELLGPPMKSLLQCNWKVPAENFIGDG
YHVGWTHAAALSQIGGELAGLAGNRADIPFDDLGLQFTTRHGHGFGVIDN
AAAGLHIKREGWTKFLEDTRGEVRRKFGPERERLYLGHWNCSIFPNCSFL
YGTNTFKIWHPRGPHEIEVWTYTIVPRDADPATKSMIQREAIRTFGTAGT
LESDDGENMSSATYINRGVITRNGRMNSTMGVGYEGPHPVYPGIVGISFI
GETSYRGFYRFWKEMIDAPDWASVKANDDTWDSVFPNRNFWNEKLN

Ligand information

• Ligand ID: BNL
• InChI: InChI=1S/C12H10/c1-3-7-11(8-4-1)12-9-5-2-6-10-12/h1-10H
• InChIKey: ZUOUZKKEUPVFJK-UHFFFAOYSA-N
• SMILES:
  ACDLabs 11.02: c1cc(ccc1)c2ccccc2
  CACTVS 3.352
  OpenEye OEToolkits 1.7.0: c1ccc(cc1)c2ccccc2
• Formula: C12 H10
• Name: BIPHENYL
• ChEMBL: CHEMBL14092
• ZINC: ZINC000000968250
• PDB chain: 2gbx Chain C Residue 458

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2gbx Structural investigations of the ferredoxin and terminal oxygenase components of the biphenyl 2,3-dioxygenase from Sphingobium yanoikuyae B1.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): D204 G205 H207 V208 L223 L260 H293 N295
• Binding residue (residue number reindexed from 1): D199 G200 H202 V203 L218 L255 H288 N290
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): H103 D204 H207 H212 D360
• Catalytic site (residue number reindexed from 1): H98 D199 H202 H207 D355

Gene Ontology

Molecular Function

• GO:0005506 iron ion binding
• GO:0046872 metal ion binding
• GO:0051213 dioxygenase activity
• GO:0051537 2 iron, 2 sulfur cluster binding

Biological Process

• GO:0009056 catabolic process
• GO:0044237 cellular metabolic process

External links

• PDB: RCSB:2gbx, PDBe:2gbx, PDBj:2gbx
• PDBsum: 2gbx
• PubMed: 17349044
• UniProt: A2TC87