Structure of PDB 6eyc Chain 3 Binding Site BS02

Receptor Information
>6eyc Chain 3 (length=605) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TFFAPDAVFGDRVRRFQEFLDTFTSYRDSVRSIQVYNSNNAANYNDDQDI
LPHRIIISLDDLREFDRSFWSGILVEPAYFIPPAEKALTDLADSMDDVPH
HPWKLSFKGSFGAHALSPRTLTAQHLNKLVSVEGIVTKTSLVRPKLIRSV
HYAAKTGRFHYRDYTDATTTLTTRIPTPAIYPTEDTEGNKLTTEYGYSTF
IDHQRITVQEMPEMAPAGQLPRSIDVILDDDLVDKTKPGDRVNVVGVFKS
LGAGGMNQSNLIGFKTLILGNTVYPLHARSTGVAARQMLTDFDIRNINKL
SKKKDIFDILSQSLAPSIYGHDHIKKAILLMLMGGVEKNLENGSHLRGDI
NILMVGDPSTAKSQLLRFVLNTASLAIATTGRGSSGVGLTAAVTTDRETG
ERRLEAGAMVLADRGVVCIDEFDKMTDVDRVAIHEVMEQQTVTIAKAGIH
TTLNARCSVIAAANPVFGQYDVNRDPHQNIALPDSLLSRFDLLFVVTDDI
NEIRDRSISEHVLRTHRVTIPFLRKYVQYAKERVIPQLTQEAINVIVKNY
TDLRNDDNTKKSPITARTLETLIRLATAHAKVRLSKTVNKVDAKVAANLL
RFALL
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 chain6eyc Chain 3 Residue 2002 [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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PDB6eyc ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps.
Resolution3.8 Å
Binding residue
(original residue number in PDB)		L399 E491 R542 R700 E703
Binding residue
(residue number reindexed from 1)		L346 E438 R489 R567 E570
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:0016787 hydrolase activity
GO:0016887 ATP hydrolysis activity
GO:0017116 single-stranded DNA helicase activity
GO:1904931 MCM complex 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:0006270 DNA replication initiation
GO:0006271 DNA strand elongation involved in DNA replication
GO:0006279 premeiotic DNA replication
GO:0030466 silent mating-type cassette heterochromatin formation
GO:0031509 subtelomeric heterochromatin formation
GO:0032508 DNA duplex unwinding
GO:1902975 mitotic DNA replication initiation
Cellular Component
GO:0000781 chromosome, telomeric region
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
View graph for
Cellular Component
External links
PDB RCSB:6eyc, PDBe:6eyc, PDBj:6eyc
PDBsum6eyc
PubMed29872003
UniProtP24279|MCM3_YEAST DNA replication licensing factor MCM3 (Gene Name=MCM3)

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