Structure of PDB 5dac Chain A Binding Site BS03

Receptor Information
>5dac Chain A (length=432) Species: 759272 (Thermochaetoides thermophila DSM 1495) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SKIEKLSILGVRSFGPHHPETIAFNTPLTLIVGYNGSGKTTVIECLKYAT
TGELPPNSTRNGAFIHDPDLVGEKEVRAQVKLSFRSTIGESYVVTRNIQL
LVQRNNKRTQKTLEGSLLLRNNGERTVISTRVAELDKLVSEKLGVPPAIL
DAVIFCHQDDSLWPMSEPAALKKRFDEIFEAQKYTKVIENIRLLKKKKGD
ELKILKEREVQDKANKERAEDLKDAKAKYKETHIKVETTKAAIEDLGRGM
AAVDHAIMQYHSKMMEQINRTIAELWQSTYQGTDIDTIQIRSDVESTTSS
DSGTRRNYNYRVSMVKGDTEMDMRGRCSAGQKVLASIIIRLALAESFCAN
CGLIALDQPTTNLDSDNIRSLAESLHGIIKARQAQGNLQLIVITHDEEFL
KYMQCSDFCDDFYRVKRDEKQNSVIVRESITR
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 chain5dac Chain A Residue 1402 [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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PDB5dac Structural mechanism of ATP-dependent DNA binding and DNA end bridging by eukaryotic Rad50.
Resolution2.503 Å
Binding residue
(original residue number in PDB)		R13 S14 N36 G37 G39 K40 T41 T42 A64 H1275 R1297
Binding residue
(residue number reindexed from 1)		R12 S13 N35 G36 G38 K39 T40 T41 A63 H395 R417
Annotation score4
Enzymatic activity
Enzyme Commision number 3.6.-.-
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:5dac, PDBe:5dac, PDBj:5dac
PDBsum5dac
PubMed26896444
UniProtG0SHW7|RAD50_CHATD DNA repair protein RAD50 (Gene Name=RAD50)

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