Structure of PDB 5xvd Chain L Binding Site BS01

Receptor Information

>5xvd Chain L (length=551) Species: 1080067 (Citrobacter sp. S-77)

SQRITIDPVTRIEGHLRIDCEIENGVVSKAWASGTMWRGMEEIVKNRDPR
DAWMIVQRICGVCTTTHAISSVRAAESALNIDVPVNAQYIRNIILAAHTT
HDHIVHFYQLSALDWVDITSALKADPAKASAMLNGVSTWHLNSAEEFTKV
QNKIKDLVASGQLGIFANGCWGHPAMQLPPEVNLIAVAHYLQALECQRDA
NRVVALLGGKTPHIQNLAVGGVANPINLDGLGVLNLERLMYIKSFIDKLS
DFVEQVYKVDTAVIAAFYPEWLERGQGAVNYLSAPEFPTDGKNGSFLFPG
GYITDADLSTYRPITSHSDEYLIKGIQESAKHAWYKDEAPQAPWEGTTVP
DYTGWSDDGKYSWVKAPTFYGKTVEVGPLANMLCKLAAKRESTHAKLNEI
VAIYTKLTGKTIEVAQLHSTLGRIIGRTVHCCELQNVLQDQYNALIVNIG
KGDHTTFVKPDIPATGEFKGVGFLEAPRGMLSHWMVIKDGIISNYQAVVP
STWNSGPRNFNDEVGPYERSLVGTPIADPNKPLEVVRTIHSFDPCMSCAV
H

Ligand information

• Ligand ID: MG
• InChI: InChI=1S/Mg/q+2
• InChIKey: JLVVSXFLKOJNIY-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mg+2]
  CACTVS 3.341: [Mg++]
• Formula: Mg
• Name: MAGNESIUM ION
• DrugBank: DB01378
• PDB chain: 5xvd Chain L Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5xvd Redox-dependent conformational changes of a proximal [4Fe-4S] cluster in Hyb-type [NiFe]-hydrogenase to protect the active site from O2.
• Resolution: 1.57 Å
• Binding residue (original residue number in PDB): E42 A498 H552
• Binding residue (residue number reindexed from 1): E41 A497 H551
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): E14 C61 C64 H68 R479 S502 C546 C549
• Catalytic site (residue number reindexed from 1): E13 C60 C63 H67 R478 S501 C545 C548
• Enzyme Commision number: 1.12.99.6: hydrogenase (acceptor).

Gene Ontology

Molecular Function

• GO:0008901 ferredoxin hydrogenase activity
• GO:0016151 nickel cation binding
• GO:0016491 oxidoreductase activity
• GO:0046872 metal ion binding

Cellular Component

• GO:0005886 plasma membrane

External links

• PDB: RCSB:5xvd, PDBe:5xvd, PDBj:5xvd
• PDBsum: 5xvd
• PubMed: 30328414
• UniProt: A0A3B6UEQ1