Structure of PDB 3wv7 Chain A Binding Site BS01

Receptor Information

>3wv7 Chain A (length=201) Species: 79929 (Methanothermobacter marburgensis str. Marburg)

KVPHGEVTLVGAGRLGFRTALNLMQIHRGGPERIKVIDGQKVSADDLIFR
LMGAKIGEYKVKFIESLACDGFSRTVQGIPEYITGDNLRLIGGDVVCVEI
AGGDTLPITTEIIRYAQERGAATISTMGVFGIGEEDVSVVDIDEADPENP
IAAYLQAEGIHEHVLVGTGKLIRDWEPVTPHVLDRVSEVMTAEILKLLRG
A

Ligand information

• Ligand ID: ADP
• InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
• InChIKey: XTWYTFMLZFPYCI-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
• Formula: C10 H15 N5 O10 P2
• Name: ADENOSINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL14830
• DrugBank: DB16833
• ZINC: ZINC000012360703
• PDB chain: 3wv7 Chain A Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3wv7 Protein-pyridinol thioester precursor for biosynthesis of the organometallic acyl-iron ligand in [Fe]-hydrogenase cofactor
• Resolution: 1.6 Å
• Binding residue (original residue number in PDB): G22 R23 L24 D47 K69 Y91 I92 I109 A110
• Binding residue (residue number reindexed from 1): G13 R14 L15 D38 K60 Y82 I83 I100 A101
• Annotation score: 4

Enzymatic activity

• Enzyme Commision number: 2.7.7.-

Gene Ontology

Molecular Function

• GO:0005524 ATP binding

External links

• PDB: RCSB:3wv7, PDBe:3wv7, PDBj:3wv7
• PDBsum: 3wv7
• PubMed: 25882909
• UniProt: D9PY12