Structure of PDB 7pt7 Chain D Binding Site BS02

Receptor Information

>7pt7 Chain D (length=668) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

LRIIWGTNVSIQECTTNFRNFLMSFKYKFRKILDEREEFINNTTDEELYY
IKQLNEMRELGTSNLNLDARNLLAYKQTEDLYHQLLNYPQEVISIMDQTI
KDCMVSLIVDNNLDYDLDEIETKFYKVRPYNVGSCKGMRELNPNDIDKLI
NLKGLVLRSTPVIPDMKVAFFKCNVCDHTMAVEIDRGVIQEPARCERIDC
NEPNSMSLIHNRCSFADKQVIKLQETPDFVPDGQTPHSISLCVYDELVDS
CRAGDRIEVTGTFRSIPIRANSRQRVLKSLYKTYVDVVHVKKVSDKRLDV
DTSTIEQELMQNKVDHNEVEEVRQITDQDLAKIREVAAREDLYSLLARSI
APSIYELEDVKKGILLQLFGGTNKTFTKGGRYRGDINILLCGDPSTSKSQ
ILQYVHKITPRGVYTSGKGSSAVGLTAYITRDVDTKQLVLESGALVLSDG
GVCCIDEFDKMSDSTRSVLHEVMEQQTISIAKAGIITTLNARSSILASAN
PIGSRYNPNLPVTENIDLPPPLLSRFDLVYLVLDKVDEKNDRELAKHLTN
LYLEDKPEHISQDDVLPVEFLTMYISYAKEHIHPIITEAAKTELVRAYVG
MRKKRITATTRQLESMIRLAEAHAKMKLKNVVELEDVQEAVRLIRSAIKD
YATDPKTGKIDMNLVQTG

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

7pt7 Chain D Residue 1102 [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	7pt7 The structural basis of Cdc7-Dbf4 kinase dependent targeting and phosphorylation of the MCM2-7 double hexamer.
Resolution	3.8 Å
Binding residue (original residue number in PDB)	I530 Y531 P570 S571 S573 K574 S575 Q576
Binding residue (residue number reindexed from 1)	I354 Y355 P394 S395 S397 K398 S399 Q400
Annotation score	5

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:0032508	DNA duplex unwinding
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

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Molecular Function

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Cellular Component

External links

PDB	RCSB:7pt7, PDBe:7pt7, PDBj:7pt7
PDBsum	7pt7
PubMed	35614055
UniProt	P30665\|MCM4_YEAST DNA replication licensing factor MCM4 (Gene Name=MCM4)

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