Structure of PDB 7zr1 Chain D Binding Site BS03

Receptor Information
>7zr1 Chain D (length=780) Species: 209285 (Thermochaetoides thermophila) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SKIEKLSILGVRSFGPHHPETIAFNTPLTLIVGYNGSGKTTVIECLKYAT
TGELPPNSTRNGAFIHDPDLVGEKEVRAQVKLSFRSTIGESYVVTRNIQL
LVQRNNKRTQKTLEGSLLLRNNGERTVISTRVAELDKLVSEKLGVPPAIL
DAVIFCHQDDSLWPMSEPAALKKRFDEIFEAQKYTKVIENIRLLKKKKGD
ELKILKEREVQDKANKERAEKVDRLMAQLTREILEAREKCNELSKQMEEE
SAKIKDKYEQANSFLKIMNDLQTKTEKLEYKKDAIVELRSRIEELPDPDE
VLRNTLDEYEQTINRIVADRDHKAAQFHDLQAELKSARDQHTAKAAEQGK
HQSDKEKYERQLVARERMIREAAERHEIRGYNGDLDDRRIAIFNERIQKI
LNDKRRELERLQKEQKVAAERDAIAQTVSELNMINSEIQEYLDRGGPSSL
AANQRAIANLETQMANLEGEMRELTVQINKLNKEIDNSDAKKRNIADNLT
YRKNLREKDALEREIAELEARNAQEDYDRLIKEAHYLEAHRSKLNADRER
LMGMMSTKDEEFRRLNEEYELDLKDAKAKYKETHIKVETTKAAIEDLGRG
MAAVDHAIMQYHSKMMEQINRTIAELWQSTYQGTDIDTIQIRSDVESTTS
SDSGTRRNYNYRVSMVKGDTEMDMRGRCSAGQKVLASIIIRLALAESFCA
NCGLIALDEPTTNLDSDNIRSLAESLHGIIKARQAQGNLQLIVITHDEEF
LKYMQCSDFCDDFYRVKRDEKQNSVIVRES
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 chain7zr1 Chain D 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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PDB7zr1 Cryo-EM structure of the Mre11-Rad50-Nbs1 complex reveals the molecular mechanism of scaffolding functions.
Resolution4.0 Å
Binding residue
(original residue number in PDB)		N36 G37 G39 K40 T41 T42 Q159
Binding residue
(residue number reindexed from 1)		N35 G36 G38 K39 T40 T41 Q158
Annotation score4
Enzymatic activity
Enzyme Commision number 3.6.-.-
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003690 double-stranded DNA binding
GO:0003691 double-stranded telomeric DNA binding
GO:0005085 guanyl-nucleotide exchange factor activity
GO:0016787 hydrolase activity
GO:0016887 ATP hydrolysis activity
GO:0043047 single-stranded telomeric DNA binding
GO:0046872 metal ion binding
GO:0051880 G-quadruplex DNA binding
Biological Process
GO:0000722 telomere maintenance via recombination
GO:0000723 telomere maintenance
GO:0006281 DNA repair
GO:0006302 double-strand break repair
GO:0007004 telomere maintenance via telomerase
GO:0032508 DNA duplex unwinding
GO:0070192 chromosome organization involved in meiotic cell cycle
Cellular Component
GO:0000794 condensed nuclear chromosome
GO:0005634 nucleus
GO:0005694 chromosome
GO:0030870 Mre11 complex
GO:0032991 protein-containing complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7zr1, PDBe:7zr1, PDBj:7zr1
PDBsum7zr1
PubMed36577401
UniProtG0SHW7|RAD50_CHATD DNA repair protein RAD50 (Gene Name=RAD50)

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