Structure of PDB 5xbp Chain D Binding Site BS01

Receptor Information

>5xbp Chain D (length=444) Species: 1302548 (Diaphorobacter sp. DS2)

SYQNLVSEAGLTQKHLIHGDKELFQHEMKTIFARNWLFLTHDSLIPSPGD
YVTAKMGLDEVIVSRQNDGSVRAFLNVCRHRGKTIVHAEAGNAKGFVCNY
HGWGYGTNGELQSVPFEKELYGDAIKKKCLGLKEVPRIESFHGFIYGCFD
AEAPPLIDYLGDAAWYMEPTFKHSGGLELVGPPGKVVVKANWKTFAENFV
GDIYHVGWTHASILRVGQSVFTPLAGNAMLPPEGSGLQMTSKYGSGMSLM
WDYYAGNHSADLVPDLMAFGGAKQEKLAKEIGDVRARIYRSHLNGTIFPN
NSFLTGSAAFKVWNPIDENTTEVWTYAFVEKDMPEDLKRRLADAVQRTVG
PGGYWESDDNDNMETLSQNAKKYQSSNSDLIASLGFGKDVYGDECYPGVV
GPSGASETSYRGFYRAYQAHISSSNWAEFENASRNWHTELTKTT

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: 5xbp Chain D Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5xbp Structural and functional studies of ferredoxin and oxygenase components of 3-nitrotoluene dioxygenase from Diaphorobacter sp. strain DS2.
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): H206 H211 D360
• Binding residue (residue number reindexed from 1): H205 H210 D359
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): Y101
• Catalytic site (residue number reindexed from 1): Y100

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:5xbp, PDBe:5xbp, PDBj:5xbp
• PDBsum: 5xbp
• PubMed: 28448625
• UniProt: M9PW10