Structure of PDB 6s6v Chain D Binding Site BS02

Receptor Information
>6s6v Chain D (length=363) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKILSLRLKNLNSLKGEWKIDFTREPFASNGLFAITGPTGAGKTTLLDAI
CLALYHETPRLSNVSQSQNDLMTRDTAECLAEVEFEVKGEAYRAFWSQNR
ARNQPDGNLQVPRVELARCADGKILADKVKDKLELTATLTGLDYGRFTRS
MLLSQGQFAAFLNAKPKERAELLEELTGTEIYGQISAMVFEQHKWGYLNS
LIGSKEGDKFRKFAQGLTLDNLVHLANQQLTRLHGRYLLQRKASEALEVE
VVDTWQADAVRDTRTLSGGESFLVSLALALALSDLVSHKTRIDSLFLDEG
FGTLDSETLDTALDALDALNASGKTIGVISHVEAMKERIPVQIKVKKING
LGYSKLESTFAVK
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 chain6s6v Chain D Residue 1101 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6s6v Mechanism of DNA End Sensing and Processing by the Mre11-Rad50 Complex.
Resolution3.5 Å
Binding residue
(original residue number in PDB)		Y922 R946 T950 S952 E955
Binding residue
(residue number reindexed from 1)		Y237 R261 T265 S267 E270
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000014 single-stranded DNA endodeoxyribonuclease activity
GO:0004519 endonuclease activity
GO:0004527 exonuclease activity
GO:0004529 DNA exonuclease activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008296 3'-5'-DNA exonuclease activity
GO:0016887 ATP hydrolysis activity
GO:1990238 double-stranded DNA endonuclease activity
Biological Process
GO:0006260 DNA replication
GO:0006274 DNA replication termination
GO:0006281 DNA repair
GO:0006302 double-strand break repair
GO:0006310 DNA recombination
Cellular Component
GO:1990391 DNA repair complex

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6s6v, PDBe:6s6v, PDBj:6s6v
PDBsum6s6v
PubMed31492634
UniProtP13458|SBCC_ECOLI Nuclease SbcCD subunit C (Gene Name=sbcC)

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