Structure of PDB 8p62 Chain 2 Binding Site BS01

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 2 Residue 901 [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)		Y506 P545 G546 T547 A548 K549 S550 Q551 V699
Binding residue
(residue number reindexed from 1)		Y328 P367 G368 T369 A370 K371 S372 Q373 V521
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

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Molecular Function
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Biological Process
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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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