Structure of PDB 8w7m Chain 6 Binding Site BS01

Receptor Information
>8w7m Chain 6 (length=613) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KVDDVTGEKVREAFEQFLEDFSVQSTDTGEVEKVYRAQIEFMKIYDLNTI
YIDYQHLSMRENGALAMAISEQYYRFLPFLQKGLRRVVRKYAPELLNTSS
PEQTERVFQISFFNLPTVHRIRDIRSEKIGSLLSISGTVTRTSEVRPELY
KASFTCDMCRAIVDNVEQSFKYTEPTFCPNPSCENRAFWTLNVTRSRFLD
WQKVRIQENANEIPTGSMPRTLDVILRGDSVERAKPGDRCKFTGVEIVVP
DVTQLGLNSGVTGLLGVRDLTYKISFLACHVISIGDQEVFLNSLSSDEIN
ELKEMVKDEHIYDKLVRSIAPAVFGHEAVKKGILLQMLGGVHKSTVEGIK
LRGDINICVVGDPSTSKSQFLKYVVGFAPRSVYTSGKASSAAGLTAAVVR
DEDYTIEAGALMLADNGICCIDEFDKMDISDQVAIHEAMEQQTISIAKAG
IHATLNARTSILAAANPVGGRYNRKLSLRGNLNMTAPIMSRFDLFFVILD
DCNEKIDTELASHIVDLHMKRDEAIEPPFSAEQLRRYIKYARTFKPILTK
EARSYLVEKYKELRKDDASYRITVRQLESMIRLSEAIARANCVDEITPSF
IAEAYDLLRQSII
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 chain8w7m 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

[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]
PDB8w7m Synergism between CMG helicase and leading strand DNA polymerase at replication fork.
Resolution4.12 Å
Binding residue
(original residue number in PDB)		V797 R798 E801
Binding residue
(residue number reindexed from 1)		V574 R575 E578
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
GO:1990518 single-stranded 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:0032508 DNA duplex unwinding
GO:1902969 mitotic DNA replication
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:8w7m, PDBe:8w7m, PDBj:8w7m
PDBsum8w7m
PubMed37730685
UniProtP53091|MCM6_YEAST DNA replication licensing factor MCM6 (Gene Name=MCM6)

[Back to BioLiP]