Structure of PDB 8umv Chain D Binding Site BS03

Receptor Information
>8umv Chain D (length=329) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AKPVPWVEKYRPKCVDEVAFQEEVVAVLKKSLEGADLPNLLFYGPPGTGK
TSTILAAARELFGPELFRLRVLELNASDERGIQVVREKVKNFAQLTVSGS
RSDGKPCPPFKIVILDEADSMTSAAQAALRRTMEKESKTTRFCLICNYVS
RIIEPLTSRCSKFRFKPLSDKIQQQRLLDIAKKENVKISDEGIAYLVKVS
EGDLRKAITFLQSATRLTGGKEITEKVITDIAGVIPAEKIDGVFAACQSG
SFDKLEAVVKDLIDEGHAATQLVNQLHDVVVENNLSDKQKSIITEKLAEV
DKCLADGADEHLQLISLCATVMQQLSQNC
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 chain8umv Chain D Residue 402 [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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PDB8umv Cryo-EM reveals a nearly complete PCNA loading process and unique features of the human alternative clamp loader CTF18-RFC.
Resolution2.75 Å
Binding residue
(original residue number in PDB)		V41 R45 A53 P80 G81 T82 G83 K84 T85 S86 N181 L238 R239
Binding residue
(residue number reindexed from 1)		V7 R11 A19 P46 G47 T48 G49 K50 T51 S52 N147 L204 R205
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
GO:0017116 single-stranded DNA helicase activity
Biological Process
GO:0006260 DNA replication
GO:0006261 DNA-templated DNA replication
GO:0006271 DNA strand elongation involved in DNA replication
GO:0006281 DNA repair
GO:0032508 DNA duplex unwinding
GO:1900264 positive regulation of DNA-directed DNA polymerase activity
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005663 DNA replication factor C 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:8umv, PDBe:8umv, PDBj:8umv
PDBsum8umv
PubMed38669181
UniProtP35249|RFC4_HUMAN Replication factor C subunit 4 (Gene Name=RFC4)

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