Structure of PDB 6f0l Chain D Binding Site BS02

Receptor Information

>6f0l Chain D (length=634) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

SFDRPEIYSAPVLQGESPNDDDNTEIIKSFKNFILEFRLDSQFIYRDQLR
NNILVKNYSLTVNMEHLIGYNEDIYKKLSDEPSDIIPLFETAITQVAKRI
SILSRAQSANSLPTFQLILNSNANQIPLRDLDSEHVSKIVRLSGIIISTS
VLSSRATYLSIMCRNCRHTTSITINNFNNTVSLPRSCLSTIESESSMANE
KNCGPDPYIIIHESSKFIDQQFLKLQEIPELVPVGEMPRNLTMTCDRYLT
NKVIPGTRVTIVGIYSIYNSKGVAIRTPYIKILGIQSDVVTMFTEEEEEE
FLQLSRNPKLYEILTNSIAPSIFGNEDIKKAIVCLLMGGSKKILPDGMRL
RGDINVLLLGDPGTAKSQLLKFVEKVSPIAVYTSGKGSSAAGLTASVQRD
PMTREFYLEGGAMVLADGGVVCIDEFDKMRDEDRVAIHEAMEQQTISIAK
AGITTVLNSRTSVLAAANPIYGRYDDLKSPGDNIDFQTTILSRFDMIFIV
KDDHNEERDISIANHVINIHTGNANAMQNQQEENGSEISIEKMKRYITYC
RLKCAPRLSPQAAEKLSSNFVTIRKQLLINELESTERPITIRQLEAIIRI
TESLAKLELSPIAQERHVDEAIRLFQASTMDAAS

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

6f0l Chain B 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	6f0l Cryo-EM structure of a licensed DNA replication origin.
Resolution	4.77 Å
Binding residue (original residue number in PDB)	R549 I650 R651
Binding residue (residue number reindexed from 1)	R493 I591 R592
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: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

	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:0006279	premeiotic DNA replication
GO:0006368	transcription elongation by RNA polymerase II
GO:0030174	regulation of DNA-templated DNA replication initiation
GO:0031507	heterochromatin formation
GO:0031509	subtelomeric heterochromatin formation
GO:0032508	DNA duplex unwinding
GO:0033260	nuclear DNA replication

	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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Cellular Component

External links

PDB	RCSB:6f0l, PDBe:6f0l, PDBj:6f0l
PDBsum	6f0l
PubMed	29269875
UniProt	P29496\|MCM5_YEAST Minichromosome maintenance protein 5 (Gene Name=MCM5)

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