Structure of PDB 6bxo Chain B Binding Site BS01

Receptor Information

>6bxo Chain B (length=320) Species: 1392998 (Candidatus Methanoperedens nitroreducens)

QFDFDLERILKTIKDKNCKKVGLQFPEGLKRQAINIAREIEEKTRANVII
SGNPCFGACDIDTILAGSVDILFHFGHAGMGEYENVVFIEARSNIDIIPA
VKTALNLLKANRIGLITTVQHVHKLEEACKVIKEYGKECVIGKGDPRAIY
PGQVLGCNFTAARVDCEEFIYIGSGIFHPLGVAIATKKRVIAADPFLNQA
VEVSPERFLRKRGGYIAKATGAKIFGIIVSTKSGQYRMKLAQKLKEIADK
HGKIGYIILMDLVTPEQLLAFKADAYVNTACPRITIDDAERFHAPVLTPQ
EFEIVLGERRWENMEMDEMI

Ligand information

• Ligand ID: SF4
• InChI: InChI=1S/4Fe.4S
• InChIKey: LJBDFODJNLIPKO-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: [S]12[Fe]3[S]4[Fe]1[S]5[Fe]2[S]3[Fe]45
  CACTVS 3.385: S1[Fe]S[Fe]1.S2[Fe]S[Fe]2
• Formula: Fe4 S4
• Name: IRON/SULFUR CLUSTER
• PDB chain: 6bxo Chain B Residue 900

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6bxo Organometallic and radical intermediates reveal mechanism of diphthamide biosynthesis.
• Resolution: 1.655 Å
• Binding residue (original residue number in PDB): C61 R149 G158 C159 C283
• Binding residue (residue number reindexed from 1): C59 R147 G156 C157 C281
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.5.1.108: 2-(3-amino-3-carboxypropyl)histidine synthase.

Gene Ontology

Molecular Function

• GO:0016740 transferase activity
• GO:0046872 metal ion binding
• GO:0051539 4 iron, 4 sulfur cluster binding
• GO:0090560 2-(3-amino-3-carboxypropyl)histidine synthase activity

Biological Process

• GO:0017183 protein histidyl modification to diphthamide

External links

• PDB: RCSB:6bxo, PDBe:6bxo, PDBj:6bxo
• PDBsum: 6bxo
• PubMed: 29590073
• UniProt: A0A062UZ78