Structure of PDB 8p5e Chain 4 Binding Site BS01

Receptor Information
>8p5e Chain 4 (length=592) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TNVSIQECTTNFRNFLMSFKYKFRKILDERELYYIKQLNEMRELGTSNLN
LDARNLLAYKQTEDLYHQLLNYPQEVISIMDQTIKDCMVSLIVDLDEIET
KFYKVRPYNVGSCKGMRELNPNDIDKLINLKGLVLRSTPVIPDMKVAFFK
CNVCDHTMAVEIDRGVIQEPARCERIDCNEPNSMSLIHNRCSFADKQVIK
LQETPDFVPDGQTPHSISLCVYDELVDSCRAGDRIEVTGTFRSIPIRANS
RQRVLKSLYKTYVDVVHVKKVQDLAKIREVAAREDLYSLLARSIAPSIYE
LEDVKKGILLQLFGGTNKTFTKGGRYRGDINILLCGDPSTSKSQILQYVH
KITPRGVYTSGGLTAYITRDVDTKQLVLESGALVLSDGGVCCIDEFDKMS
DSTRSVLHEVMEQQTISIAKAGIITTLNARSSILASANPIGSRYNPNLPV
TENIDLPPPLLSRFDLVYLVLDKVDEKNDRELAKHLTNLYLVLPVEFLTM
YISYAKEHIHPIITEAAKTELVRAYVGMRKMGDDSRSDEKRITATTRQLE
SMIRLAEAHAKMKLKNVVELEDVQEAVRLIRSAIKDYATDPK
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=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)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain8p5e Chain 4 Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB8p5e Unwinding of a eukaryotic origin of replication visualized by cryo-EM.
Resolution3.9 Å
Binding residue
(original residue number in PDB)		P570 S571 T572 S573 K574 S575
Binding residue
(residue number reindexed from 1)		P338 S339 T340 S341 K342 S343
Annotation score5
Enzymatic activity
Enzyme Commision number 3.6.4.12: DNA helicase.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003678 DNA helicase activity
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:0009378 four-way junction helicase activity
GO:0016787 hydrolase activity
GO:0016887 ATP hydrolysis activity
GO:0017116 single-stranded DNA helicase activity
GO:0043138 3'-5' DNA helicase activity
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:0006270 DNA replication initiation
GO:0006271 DNA strand elongation involved in DNA replication
GO:0006279 premeiotic DNA replication
GO:0033260 nuclear DNA replication
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
GO:0097373 MCM core complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8p5e, PDBe:8p5e, PDBj:8p5e
PDBsum8p5e
PubMed38760633
UniProtP30665|MCM4_YEAST DNA replication licensing factor MCM4 (Gene Name=MCM4)

[Back to BioLiP]