Structure of PDB 6rvh Chain B Binding Site BS02

Receptor Information

>6rvh Chain B (length=443) Species: 274 (Thermus thermophilus)

MGKRMVVVGGVAGGASAAAKAKRENPELEVVVYEKSGWVSYGACGLPYVL
SGEIPRLERLVARTPEEFRKQGVLVHTRHEVVDVDYELRTLTVHDHAEGR
TFQDRFDHLVLATGARPSLPPIPGTEQEGVYTLRTMEDGERLLKALPQAR
RAAILGAGYIGLEAAEAFRKRGLQVTLLEAKDRPLPHWDPEVGALLKEEL
ERHGVEVWTGVKVEAFRGMGRVEAVETSEGVVPADLVLLATGIRPNTELA
QAMGVALGPTGAIATDERMRTNLEGVYAAGDVAESFHRVLKRPYWLPLGD
VANKHGRTAGSVIAGREARFLGVVGTAIFKAFDLAVATTGLSLEGALKEG
FWAKKVFIQSRDGAHYYPGSGPLWVELVYEEGTGRLLGGAVVARGHGALR
IDVLAALLHREGSVEDLLALDLAYAPPFSPVWDPLLIAAQQAR

Ligand information

• Ligand ID: VK3
• InChI: InChI=1S/C11H8O2/c1-7-6-10(12)8-4-2-3-5-9(8)11(7)13/h2-6H,1H3
• InChIKey: MJVAVZPDRWSRRC-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341
  OpenEye OEToolkits 1.5.0: CC1=CC(=O)c2ccccc2C1=O
  ACDLabs 10.04: O=C2c1c(cccc1)C(=O)C(=C2)C
• Formula: C11 H8 O2
• Name: MENADIONE;
  VITAMIN K3;
  2-METHYL-1,4-NAPHTHALENEDIONE
• ChEMBL: CHEMBL590
• DrugBank: DB00170
• ZINC: ZINC000000001677
• PDB chain: 6rvh Chain B Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6rvh Characterization and X-ray structure of the NADH-dependent coenzyme A disulfide reductase from Thermus thermophilus.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): A364 H365 P430 V431
• Binding residue (residue number reindexed from 1): A364 H365 P430 V431
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): V39 C44 E53 E58 Y159 E163 A425 P430
• Catalytic site (residue number reindexed from 1): V39 C44 E53 E58 Y159 E163 A425 P430
• Enzyme Commision number: 1.6.-.-

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0016491 oxidoreductase activity

External links

• PDB: RCSB:6rvh, PDBe:6rvh, PDBj:6rvh
• PDBsum: 6rvh
• PubMed: 31520616
• UniProt: Q72HK3