Structure of PDB 7thv Chain B Binding Site BS01

Receptor Information
>7thv Chain B (length=314) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QLPWVEKYRPQVLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTT
SVHCLAHELLGRSYADGVLELNASDDRGIDVVRNQIKHFAQKKLHLPPGK
HKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSR
CAILRYSKLSDEDVLKRLLQIIKLEDVKYTNDGLEAIIFTAEGDMRQAIN
NLQSTVAGHGLVNADNVFKIVDSPHPLIVKKMLLASNLEDSIQILRTDLW
KKGYSSIDIVTTSFRVTKNLAQVKESVRLEMIKEIGLTHMRILEGVGTYL
QLASMLAKIHKLNN
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 chain7thv Chain B Residue 401 [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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PDB7thv Cryo-EM structures reveal high-resolution mechanism of a DNA polymerase sliding clamp loader.
Resolution4.0 Å
Binding residue
(original residue number in PDB)		V12 P17 V24 G54 K55 T56 T57 N145 M202 R203
Binding residue
(residue number reindexed from 1)		V5 P10 V17 G47 K48 T49 T50 N138 M195 R196
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003689 DNA clamp loader activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016887 ATP hydrolysis activity
Biological Process
GO:0000077 DNA damage checkpoint signaling
GO:0006260 DNA replication
GO:0006261 DNA-templated DNA replication
GO:0006271 DNA strand elongation involved in DNA replication
GO:0006272 leading strand elongation
GO:0006281 DNA repair
GO:0007062 sister chromatid cohesion
GO:0007064 mitotic sister chromatid cohesion
GO:0090618 DNA clamp unloading
Cellular Component
GO:0005634 nucleus
GO:0005663 DNA replication factor C complex
GO:0005829 cytosol
GO:0031389 Rad17 RFC-like complex
GO:0031390 Ctf18 RFC-like complex
GO:0031391 Elg1 RFC-like complex

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7thv, PDBe:7thv, PDBj:7thv
PDBsum7thv
PubMed35179493
UniProtP40339|RFC4_YEAST Replication factor C subunit 4 (Gene Name=RFC4)

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