Structure of PDB 8kg9 Chain 3 Binding Site BS03

Receptor Information

>8kg9 Chain 3 (length=637) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

DAVFGDRVRRFQEFLDTFTSYRDSVRSIQVYNSNNAANLNILPHRIIISL
DDLREFDRSFWSGILVEPAYFIPPAEKALTDLADSMDDVPHPNASAVSSR
HPWKLSFKGSFGAHALSPRTLTAQHLNKLVSVEGIVTKTSLVRPKLIRSV
HYAAKTGRFHYRDYTDATTTLTTRIPTPAIYPTEDTEGNKLTTEYGYSTF
IDHQRITVQEMPEMAPAGQLPRSIDVILDDDLVDKTKPGDRVNVVGVFKS
LGAGGMNQSNTLIGFKTLILGNTVYPLHARSTGVAARQMLTDFDIRNINK
LSKKKDIFDILSQSLAPSIYGHDHIKKAILLMLMGGVEKNLENGSHLRGD
INILMVGDPSTAKSQLLRFVLNTASLAIATTGRGSSGVGLTAAVTTDRET
GERRLEAGAMVLADRGVVCIDEFDKMTDVDRVAIHEVMEQQTVTIAKAGI
HTTLNARCSVIAAANPVFGQYDVNRDPHQNIALPDSLLSRFDLLFVVTDD
INEIRDRSISEHVLRTHRYLPPGYLEGEPVRERLNLSLAVGEDADKLVTI
PFLRKYVQYAKERVIPQLTQEAINVIVKNYTDLRNDDNTKKSPITARTLE
TLIRLATAHAKVRLSKTVNKVDAKVAANLLRFALLGE

Ligand information

Ligand ID

ADP

InChI

InChI=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

InChIKey

XTWYTFMLZFPYCI-KQYNXXCUSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.5.0	c1nc(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 3.341	Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04	O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341	Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0	c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N

Formula

C10 H15 N5 O10 P2

Name

ADENOSINE-5'-DIPHOSPHATE

PDB chain

8kg9 Chain 3 Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	8kg9 Synergism between CMG helicase and leading strand DNA polymerase at replication fork.
Resolution	4.52 Å
Binding residue (original residue number in PDB)	I371 Y372 H374 D410 P411 S412 T413 A414 K415 S416 Q417 I561
Binding residue (residue number reindexed from 1)	I319 Y320 H322 D358 P359 S360 T361 A362 K363 S364 Q365 I509
Annotation score	5

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

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Cellular Component

External links

PDB	RCSB:8kg9, PDBe:8kg9, PDBj:8kg9
PDBsum	8kg9
PubMed	37730685
UniProt	P24279\|MCM3_YEAST DNA replication licensing factor MCM3 (Gene Name=MCM3)

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