Structure of PDB 4gp6 Chain A Binding Site BS01

Receptor Information

>4gp6 Chain A (length=171) Species: 203119 (Acetivibrio thermocellus ATCC 27405)

SMKLTIPELSLVVLIGSSGSGKSTFAKKHFKPTEVISSDFCRGLVSDDEN
DQTVTGAAFDVLHYIVSKRLQLGKLTVVDATNVQESARKPLIEIAKDYHC
FPVAVVFNLPEKVCQERNKNRTDRQVEEYVIRKHTQQLKKSIKGLQREGF
RYVYILNSPEEVEEVVFERQP

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: 4gp6 Chain A Residue 1001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4gp6 Structure and mechanism of the polynucleotide kinase component of the bacterial Pnkp-Hen1 RNA repair system.
• Resolution: 2.1 Å
• Binding residue (original residue number in PDB): G18 S19 G20 K21 S22 T23 R116 R120
• Binding residue (residue number reindexed from 1): G19 S20 G21 K22 S23 T24 R117 R121
• Annotation score: 5

Enzymatic activity

• Enzyme Commision number: 2.7.1.78: polynucleotide 5'-hydroxyl-kinase.

External links

• PDB: RCSB:4gp6, PDBe:4gp6, PDBj:4gp6
• PDBsum: 4gp6
• PubMed: 23118415
• UniProt: A3DJ38