Structure of PDB 8dr0 Chain D Binding Site BS02

Receptor Information
>8dr0 Chain D (length=344) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KRKISKLAAEQSLAQQPWVEKYRPKNLDEVTAQDHAVTVLKKTLKSANLP
HMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVREK
VKNFARLTVSKPSKHDLENYPCPPYKIIILDEADSMTADAQSALRRTMET
YSGVTRFCLICNYVTRIIDPLASRCSKFRFKALDASNAIDRLRFISEQEN
VKCDDGVLERILDISAGDLRRGITLLQSASKGAQYLGDGKNITSTQVEEL
AGVVPHDILIEIVEKVKSGDFDEIKKYVNTFMKSGWSAASVVNQLHEYYI
TNDNFDTNFKNQISWLLFTTDSRLNNGTNEHIQLLNLLVKISQL
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 chain8dr0 Chain D Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8dr0 Multistep loading of a DNA sliding clamp onto DNA by replication factor C.
Resolution2.42 Å
Binding residue
(original residue number in PDB)		V28 Y31 R32 P33 T40 P67 G68 T69 G70 K71 T72 S73 N171 L228 R229
Binding residue
(residue number reindexed from 1)		V19 Y22 R23 P24 T31 P58 G59 T60 G61 K62 T63 S64 N162 L219 R220
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:0000076 DNA replication checkpoint signaling
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:0006298 mismatch 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: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:8dr0, PDBe:8dr0, PDBj:8dr0
PDBsum8dr0
PubMed35939393
UniProtP40348|RFC2_YEAST Replication factor C subunit 2 (Gene Name=RFC2)

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