Structure of PDB 8kg6 Chain 2 Binding Site BS03

Receptor Information

>8kg6 Chain 2 (length=662) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

ELTLESLSNVKANSYSEWITQPNVSRTIARELKSFLLEYTDETGRSVYGA
RIRTLGEMNSESLEVNYRHLAESKAILALFLAKCPEEMLKIFDLVAMEAT
ELHYPDYARIHSEIHVRISDFPTIYSLRELRESNLSSLVRVTGVVTRRTG
VFPQLKYVKFNCLKCGSILGPFFQDSNEEIRISFCTNCKSKGPFRVNGEK
TVYRNYQRVTLQEAPGTVPPGRLPRHREVILLADLVDVSKPGEEVEVTGI
YKNNYDGNLNAKNGFPVFATIIEANSIKRREGNTANEGEEGLDVFSWTEE
EEREFRKISRDRGIIDKIISSMAPSIYGHRDIKTAVACSLFGGVPKNVNG
KHSIRGDINVLLLGDPGTAKSQILKYVEKTAHRAVFATGQGASAVGLTAS
VRKDPITKEWTLEGGALVLADKGVCLIDEFDKMNDQDRTSIHEAMEQQSI
SISKAGIVTTLQARCSIIAAANPNGGRYNSTLPLAQNVSLTEPILSRFDI
LCVVRDLVDEEADERLATFVVDSHVRSHPENLNARQRRLQRQRKKEEEIS
PIPQELLMKYIHYARTKIYPKLHQMDMDKVSRVYADLRRESISTGSFPIT
VRHLESILRIAESFAKMRLSEFVSSYDLDRAIKVVVDSFVDAQKVSVRRQ
LRRSFAIYTLGH

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

8kg6 Chain 2 Residue 902 [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	8kg6 Synergism between CMG helicase and leading strand DNA polymerase at replication fork.
Resolution	3.07 Å
Binding residue (original residue number in PDB)	I505 Y506 P545 G546 T547 A548 K549 S550 Q551 L695 V699
Binding residue (residue number reindexed from 1)	I326 Y327 P366 G367 T368 A369 K370 S371 Q372 L516 V520
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
GO:0046872	metal ion 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:0006974	DNA damage response
GO:0032508	DNA duplex unwinding
GO:1902975	mitotic DNA replication initiation
GO:1905775	negative regulation of DNA helicase activity

	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

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Molecular Function

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Biological Process

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Cellular Component

External links

PDB	RCSB:8kg6, PDBe:8kg6, PDBj:8kg6
PDBsum	8kg6
PubMed	37730685
UniProt	P29469\|MCM2_YEAST DNA replication licensing factor MCM2 (Gene Name=MCM2)

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