Structure of PDB 2gxa Chain J Binding Site BS02

Receptor Information

>2gxa Chain J (length=270)

TEKFDFGTMVQWAYDHKYAEESKIAYEYALAAGSDSNARAFLATNSQAKH
VKDCATMVRHYLRAETQALSMPAYIKARCKLATGEGSWKSILTFFNYQNI
ELITFINALKLWLKGIPKKNCLAFIGPPNTGKSMLCNSLIHFLGGSVLSF
ANHKSHFWLASLADTRAALVDDATHACWRYFDTYLRNALDGYPVSIDRKH
KAAVQIKAPPLLVTSNIDVQAEDRYLYLHSRVQTFRFEQPCTDESGEQPF
NITDADWKSFFVRLWGRLDL

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: 2gxa Chain K Residue 10

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2gxa Mechanism of DNA translocation in a replicative hexameric helicase.
• Resolution: 3.15 Å
• Binding residue (original residue number in PDB): T437 G438 K439 S440 M441 D550 F557 N558
• Binding residue (residue number reindexed from 1): T130 G131 K132 S133 M134 D243 F250 N251
• Annotation score: 5

Enzymatic activity

• Enzyme Commision number: 3.6.4.12: DNA helicase.

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003678 DNA helicase activity
• GO:0005524 ATP binding

Biological Process

• GO:0006260 DNA replication

External links

• PDB: RCSB:2gxa, PDBe:2gxa, PDBj:2gxa
• PDBsum: 2gxa
• PubMed: 16855583
• UniProt: P03116|VE1_BPV1 Replication protein E1 (Gene Name=E1)