Structure of PDB 4ncj Chain B Binding Site BS01

Receptor Information
>4ncj Chain B (length=311) Species: 186497 (Pyrococcus furiosus DSM 3638) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKLERVTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGLYWP
LRIKDIKKDEFTKVGARDTYIDLIFEKDGTKYRITRRFLKGYSSGEIHAM
KRLVGNEWKHVTEPSSKAISAFMEKLIPYNIFLNAIYIRQGQIDAILESD
EAREKVVREVLNLDYKALAREAALSKIGELASEIFAEFTEGKYSEVVVRA
EENKVRLFVVWEGKERPLTFLSGGERIALGLAFELAMSLYLAGEISLLIL
DEPTPYLDEERRRKLITIMERYLKKIPQVILVSHDEELKDAADHVIRISL
ENGSSKVEVVS
Ligand information
Ligand IDADP
InChIInChI=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
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(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 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain4ncj Chain B Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4ncj ATP-driven Rad50 conformations regulate DNA tethering, end resection, and ATM checkpoint signaling.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		R12 S13 N32 G33 S34 G35 K36 S37 S38 K63 V64
Binding residue
(residue number reindexed from 1)		R12 S13 N32 G33 S34 G35 K36 S37 S38 K63 V64
Annotation score5
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0016887 ATP hydrolysis activity
Biological Process
GO:0006302 double-strand break repair

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4ncj, PDBe:4ncj, PDBj:4ncj
PDBsum4ncj
PubMed24493214
UniProtP58301|RAD50_PYRFU DNA double-strand break repair Rad50 ATPase (Gene Name=rad50)

[Back to BioLiP]