Structure of PDB 3vys Chain B Binding Site BS01

Receptor Information

>3vys Chain B (length=368) Species: 69014 (Thermococcus kodakarensis KOD1)

PFEAYRSREVAMKLVEKIREEAKTLDGEIRIMHVCGTHEDTVTRHGIRSL
LPENVKVVSGPGCPVCITPVEDIVAMQLIMRKAREEGEEIILTTFGDMYK
IPTPMGSFADLKSEGFDVRIVYGIFDTYRIAKENPDKTVVHFSPGFETTT
APAAGMLNVAAQEELENFKIYSVHRLTPPAVEVLLKQGTVFQGLIAPGHV
STIIGVKGWEYLTEKYGIPQVVAGFEPNDVLMAILMLIRMYKEGEARIIN
EYERAVKYEGNVVAQKMIDKFFEVVDAKWRALGVFPKSGLELRKEWKDFE
IRSFYKVEVPKNLPDLEKGCRCGAVLRGLALPTDCPLFGKTCTPRHPVGP
CMVSYEGTCQIFYKYGVL

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: 3vys Chain B Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3vys Crystal structures of the HypCD complex and the HypCDE ternary complex: transient intermediate complexes during [NiFe] hydrogenase maturation
• Resolution: 2.35 Å
• Binding residue (original residue number in PDB): C323 R324 C325 C338 L340 F341 C345 G352 C354 M355 C362
• Binding residue (residue number reindexed from 1): C320 R321 C322 C335 L337 F338 C342 G349 C351 M352 C359
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0005506 iron ion binding
• GO:0005515 protein binding
• GO:0046872 metal ion binding
• GO:0051539 4 iron, 4 sulfur cluster binding
• GO:0070025 carbon monoxide binding

Biological Process

• GO:0051604 protein maturation

External links

• PDB: RCSB:3vys, PDBe:3vys, PDBj:3vys
• PDBsum: 3vys
• PubMed: 23123111
• UniProt: Q5JII1