Structure of PDB 5f3w Chain B Binding Site BS03

Receptor Information
>5f3w Chain B (length=359) Species: 243232 (Methanocaldococcus jannaschii DSM 2661) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MSMILKEIRMNNFKSHVNSRIKFEKGIVAIIGENGSGKSSIFEAVFFALF
GAGSNFNYDTIITKGKKSVYVELDFEVNGNNYKIIREYDSGRGGAKLYKN
GKPYATTISAVNKAVNEILGVDRNMFLNSIYIKQGEIAKFLSLKPSEKLE
TVAKLLGIDEFEKCYQKMGEIVKEYEKRLERIEGEKEMSNLEKEKEKLTK
FVEYLDKVRRIFGRNGFQAYLREKYVPLIQKYLNEAFSEFDLPYSFVELT
KDFEVRVHAPNGVLTIDNLSGGEQIAVALSLRLAIANALIGNRVECIILD
EPTVYLDENRRAKLAEIFRKVKSIPQMIIITHHRELEDVADVIINVKKDG
NVSKVKING
Ligand information
Ligand IDAGS
InChIInChI=1S/C10H16N5O12P3S/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(25-10)1-24-28(18,19)26-29(20,21)27-30(22,23)31/h2-4,6-7,10,16-17H,1H2,(H,18,19)(H,20,21)(H2,11,12,13)(H2,22,23,31)/t4-,6-,7-,10-/m1/s1
InChIKeyNLTUCYMLOPLUHL-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[C@@H](O)[C@H]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
ACDLabs 12.01O=P(O)(OP(=S)(O)O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC10 H16 N5 O12 P3 S
NamePHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER;
ATP-GAMMA-S;
ADENOSINE 5'-(3-THIOTRIPHOSPHATE);
ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE);
ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE
ChEMBLCHEMBL131890
DrugBankDB02930
ZINCZINC000008295128
PDB chain5f3w Chain D Residue 1101 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5f3w ATP-dependent DNA binding, unwinding, and resection by the Mre11/Rad50 complex
Resolution3.11 Å
Binding residue
(original residue number in PDB)		Y890 L910 N914 S916 E919
Binding residue
(residue number reindexed from 1)		Y244 L264 N268 S270 E273
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0016887 ATP hydrolysis activity
Biological Process
GO:0006302 double-strand break repair

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Molecular Function
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Biological Process
External links
PDB RCSB:5f3w, PDBe:5f3w, PDBj:5f3w
PDBsum5f3w
PubMed26717941
UniProtQ58718|RAD50_METJA DNA double-strand break repair Rad50 ATPase (Gene Name=rad50)

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