Structure of PDB 5xbp Chain D Binding Site BS02

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: FES
• InChI: InChI=1S/2Fe.2S
• InChIKey: NIXDOXVAJZFRNF-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04: [Fe]1S[Fe]S1
  CACTVS 3.341
  OpenEye OEToolkits 1.5.0: S1[Fe]S[Fe]1
• Formula: Fe2 S2
• Name: FE2/S2 (INORGANIC) CLUSTER
• PDB chain: 5xbp Chain D Residue 502

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): C79 H81 R82 C99 Y101 H102 W104
• Binding residue (residue number reindexed from 1): C78 H80 R81 C98 Y100 H101 W103
• 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