Structure of PDB 5eax Chain A Binding Site BS03

Receptor Information
>5eax Chain A (length=1046) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MEPLDELDLLLLEAVPRVELLRKKADALFPETVLSRGVDNRYLVLAVETS
QNERGAEEKRLHVTASQDREHEVLCILRNGWSSVPVEPGDIVHLEGDCTS
EPWIIDDDFGYFILYPDMMISGTSVASSIRCLRRAVLSETFRGSDPATRQ
MLIGTILHEVFQKAISESFAPERLQELALQTLREVRHLKEMYRLNLSQDE
ILCEVEEYLPSFSKWAEDFMRKGPSSEFPQMQLSLPSDGRSSPCNIEVVK
SLDIEESIWSPRFGLKGKIAVTVGVKIHRDCKMKYKVMPLELKTGKESNS
IEHRSQVVLYTLLSQERREDPEAGWLLYLKTGQMYPVPANHLDKRELLKL
RNWLAASLLHRVSRAAPGEEARLSALPQIIEEEKTCKYCSQIGNCALYSR
AVEEDDASIPEAMLSKIQEETRHLQLAHLKYFSLWCLMLTLESQSKDNRK
THQSIWLTPASELEESGNCVGNLVRTEPVSRVCDGQYLHNFQRKNGPMPA
TNLMAGDRIILSGEERKLFALSKGYVKKMNKAAVTCLLDRNLSTLPATTV
FRLDREERHGDISTPLGNLSKLMESTDPSKRLRELIIDFREPQFIAYLSS
VLPHDAKDTVANILKGLNKPQRQAMKRVLLSKDYTLIVGMPGTGKTTTIC
ALVRILSACGFSVLLTSYTHSAVDNILLKLAKFKVGFLRLGQSHKVHPDI
QKFTEEEICRSRSIASLAHLEELYNSHPIVATTCMGINHPIFSRKTFDFC
IVDEASQISQPVCLGPLFFSRRFVLVGDHQQLPPLVVNREARALGMSESL
FKRLERNESAVVQLTVQYRMNRKIMSLSNKLTYAGKLECGSDRVANAVLA
LPNLKDARLSLQLYADYSDSPWLAGVLEPDNPVCFLNTDKVPAPEQVENG
GVSNVTEARLIVFLTSTFIKAGCSPSDIGVIAPYRQQLRIISDLLARSSV
GMVEVNTVDKYQGRDKSLILVSFVRSNEDGTLGELLKDWRRLNVALTRAK
HKLILLGSVSSLKRFPPLGTLFDHLNAEQLILDLPSREHESLSHIL
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 chain5eax Chain A Residue 1102 [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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PDB5eax Dna2 nuclease-helicase structure, mechanism and regulation by Rpa.
Resolution3.05 Å
Binding residue
(original residue number in PDB)		L627 N628 Q631 G654 T656 T657 K689 Y828
Binding residue
(residue number reindexed from 1)		L617 N618 Q621 G644 T646 T647 K679 Y818
Annotation score5
Enzymatic activity
Enzyme Commision number 3.1.-.-
3.6.4.12: DNA helicase.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003678 DNA helicase activity
GO:0004386 helicase activity
GO:0004518 nuclease activity
GO:0004519 endonuclease activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016887 ATP hydrolysis activity
GO:0016890 site-specific endodeoxyribonuclease activity, specific for altered base
GO:0017108 5'-flap endonuclease activity
GO:0017116 single-stranded DNA helicase activity
GO:0043139 5'-3' DNA helicase activity
GO:0046872 metal ion binding
GO:0051539 4 iron, 4 sulfur cluster binding
Biological Process
GO:0000076 DNA replication checkpoint signaling
GO:0000723 telomere maintenance
GO:0000729 DNA double-strand break processing
GO:0006259 DNA metabolic process
GO:0006260 DNA replication
GO:0006264 mitochondrial DNA replication
GO:0006281 DNA repair
GO:0006284 base-excision repair
GO:0032508 DNA duplex unwinding
GO:0033567 DNA replication, Okazaki fragment processing
GO:0043137 DNA replication, removal of RNA primer
GO:0043504 mitochondrial DNA repair
GO:0045740 positive regulation of DNA replication
GO:0090304 nucleic acid metabolic process
GO:1902990 mitotic telomere maintenance via semi-conservative replication
Cellular Component
GO:0000781 chromosome, telomeric region
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005739 mitochondrion
GO:0005760 gamma DNA polymerase complex
GO:0042645 mitochondrial nucleoid

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5eax, PDBe:5eax, PDBj:5eax
PDBsum5eax
PubMed26491943
UniProtQ6ZQJ5|DNA2_MOUSE DNA replication ATP-dependent helicase/nuclease DNA2 (Gene Name=Dna2)

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