Structure of PDB 8p62 Chain 2 Binding Site BS03

Receptor Information
>8p62 Chain 2 (length=662) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EELTLESLSNVKANSYSEWITQPNVSRTIARELKSFLLEYTDETGRSVYG
ARIRTLGEMNSESLEVNYRHLAESKAILALFLAKCPEEMLKIFDLVAMEA
TELHYPDYARIHSEIHVRISDFPTIYSLRELRESNLSSLVRVTGVVTRRT
GVFPQLKYVKFNCLKCGSILGPFFQDSNEEIRISFCTNCKSKGPFRVNGE
KTVYRNYQRVTLQEAPGTVPPGRLPRHREVILLADLVDVSKPGEEVEVTG
IYKNNYDGNLNAKNGFPVFATIIEANSIKRREGNTANEGEEGLDVFSWTE
EEEREFRKISRDRGIIDKIISSMAPSIYGHRDIKTAVACSLFGGVPKNVN
GKHSIRGDINVLLLGDPGTAKSQILKYVEKTAHRAVFATGQGASAVGLTA
SVRKDPITKEWTLEGGALVLADKGVCLIDEFDKMNDQDRTSIHEAMEQQS
ISISKAGIVTTLQARCSIIAAANPNGGRYNSTLPLAQNVSLTEPILSRFD
ILCVVRDLVDEEADERLATFVVDSHVRSHPENLNARQRRLQRQRKKEEEI
SPIPQELLMKYIHYARTKIYPKLHQMDMDKVSRVYADLRRESISTGSFPI
TVRHLESILRIAESFAKMRLSEFVSSYDLDRAIKVVVDSFVDAQKVSVRR
QLRRSFAIYTLG
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain8p62 Chain 5 Residue 1701 [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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PDB8p62 Unwinding of a eukaryotic origin of replication visualized by cryo-EM.
Resolution3.9 Å
Binding residue
(original residue number in PDB)		R676 R808 E811
Binding residue
(residue number reindexed from 1)		R498 R603 E606
Annotation score5
Enzymatic activity
Enzyme Commision number 3.6.4.12: DNA helicase.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0003688 DNA replication origin binding
GO:0003697 single-stranded DNA binding
GO:0004386 helicase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008270 zinc ion binding
GO:0016787 hydrolase activity
GO:0016887 ATP hydrolysis activity
GO:0017116 single-stranded DNA helicase activity
GO:0043138 3'-5' DNA helicase activity
GO:0046872 metal ion binding
Biological Process
GO:0000727 double-strand break repair via break-induced replication
GO:0006260 DNA replication
GO:0006267 pre-replicative complex assembly involved in nuclear cell cycle DNA replication
GO:0006268 DNA unwinding involved in DNA replication
GO:0006271 DNA strand elongation involved in DNA replication
GO:0006279 premeiotic DNA replication
GO:0006974 DNA damage response
GO:1902975 mitotic DNA replication initiation
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005656 nuclear pre-replicative complex
GO:0005737 cytoplasm
GO:0031261 DNA replication preinitiation complex
GO:0031298 replication fork protection complex
GO:0042555 MCM complex
GO:0043596 nuclear replication fork
GO:0071162 CMG complex

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8p62, PDBe:8p62, PDBj:8p62
PDBsum8p62
PubMed38760633
UniProtP29469|MCM2_YEAST DNA replication licensing factor MCM2 (Gene Name=MCM2)

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