Structure of PDB 2gbw Chain E Binding Site BS01

Receptor Information

>2gbw Chain E (length=449) Species: 13690 (Sphingobium yanoikuyae)

TLVDTVNASQSRQVFWDEDVYALEIERIFSRAWLMLGHESLVPKPGDFIT
TYMAEDKVILSHQSDGTFRAFINSCSHRGNQICHADSGNAKAFVCNYHGW
VFGQDGSLVDVPLESRCYHNSLDKQKLAAKSVRVETYKGFIFGCHDPEAP
SLEDYLGEFRYYLDTIWEGAGGGMELLGPPMKSLLQCNWKVPAENFIGDG
YHVGWTHAAALSQIGGELAGLAGNRADIPFDDLGLQFTTRHGHGFGVIDN
AAAGLHIKREGWTKFLEDTRGEVRRKFGPERERLYLGHWNCSIFPNCSFL
YGTNTFKIWHPRGPHEIEVWTYTIVPRDADPATKSMIQREAIRTFGTAGT
LESDDGENMSSATYINRGVITRNGRMNSTMGVGYEGPHPVYPGIVGISFI
GETSYRGFYRFWKEMIDAPDWASVKANDDTWDSVFPNRNFWNEKLNAAE

Ligand information

• Ligand ID: OXY
• InChI: InChI=1S/O2/c1-2
• InChIKey: MYMOFIZGZYHOMD-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341
  OpenEye OEToolkits 1.5.0: O=O
• Formula: O2
• Name: OXYGEN MOLECULE
• ChEMBL: CHEMBL1234886
• DrugBank: DB09140
• PDB chain: 2gbw Chain C Residue 457

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2gbw Structural investigations of the ferredoxin and terminal oxygenase components of the biphenyl 2,3-dioxygenase from Sphingobium yanoikuyae B1.
• Resolution: 1.7 Å
• Binding residue (original residue number in PDB): H207 D360
• Binding residue (residue number reindexed from 1): H202 D355
• Annotation score: 4

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:2gbw, PDBe:2gbw, PDBj:2gbw
• PDBsum: 2gbw
• PubMed: 17349044
• UniProt: A2TC87