Structure of PDB 7tfh Chain D Binding Site BS01

Receptor Information
>7tfh Chain D (length=331) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AQQPWVEKYRPKNLDEVTAQDHAVTVLKKTLKSANLPHMLFYGPPGTGKT
STILALTKELYGPDLMKSRILELNASDERGISIVREKVKNFARLTVSKPS
KHDLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNY
VTRIIDPLASRCSKFRFKALDASNAIDRLRFISEQENVKCDDGVLERILD
ISAGDLRRGITLLQSASKGAQYLGDGKNITSTQVEELAGVVPHDILIEIV
EKVKSGDFDEIKKYVNTFMKSGWSAASVVNQLHEYYITNDNFDTNFKNQI
SWLLFTTDSRLNNGTNEHIQLLNLLVKISQL
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 chain7tfh Chain D Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7tfh Cryo-EM structures reveal that RFC recognizes both the 3'- and 5'-DNA ends to load PCNA onto gaps for DNA repair.
Resolution3.09 Å
Binding residue
(original residue number in PDB)		V28 P33 V39 T40 G68 T69 G70 K71 T72 S73 L228 R229
Binding residue
(residue number reindexed from 1)		V6 P11 V17 T18 G46 T47 G48 K49 T50 S51 L206 R207
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:7tfh, PDBe:7tfh, PDBj:7tfh
PDBsum7tfh
PubMed35829698
UniProtP40348|RFC2_YEAST Replication factor C subunit 2 (Gene Name=RFC2)

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