Structure of PDB 8euf Chain Y Binding Site BS01

Receptor Information
>8euf Chain Y (length=445) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SLSLIAAHSHITGLGLDENLQPRPTSEGMVGQLQARRAAGVILKMVQNGT
IAGRAVLVAGPPSTGKTALAMGVSQSLGKDVPFTAIAGSEIFSLELSKTE
ALTQAFRKSIGIKIKEETELIEGEVVEIQIDRSITGGHKQGKLTIKTTDM
ETIYELGNKMIDGLTKEKVLAGDVISIDKASGKITKLGRSFARSRDYDAM
GADTRFVQCPEGELQKRKTVVHTVSLHEIDVINSRTQGFLALFTGDTGEI
RSEVRDQINTKVAEWKEEGKAEIVPGVLFIDEVHMLDIECFSFINRALED
EFAPIVMMATNRGVSKTRGTNYKSPHGLPLDLLDRSIIITTKSYNEQEIK
TILSIRAQEEEVELSSDALDLLTKTGVETSLRYSSNLISVAQQIAMKRKN
NTVEVEDVKRAYLLFLDSARSVKYVQENESQYIDDQGNVQISIAK
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 chain8euf Chain Y Residue 501 [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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PDB8euf Reorientation of INO80 on hexasomes reveals basis for mechanistic versatility.
Resolution3.41 Å
Binding residue
(original residue number in PDB)		H23 H25 G43 M44 V45 P77 S78 T79 G80 K81 T82 Y359 I367 R397
Binding residue
(residue number reindexed from 1)		H8 H10 G28 M29 V30 P62 S63 T64 G65 K66 T67 Y344 I352 R382
Annotation score5
Enzymatic activity
Enzyme Commision number 3.6.4.12: DNA helicase.
Gene Ontology
Molecular Function
GO:0003678 DNA helicase activity
GO:0004386 helicase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008094 ATP-dependent activity, acting on DNA
GO:0016787 hydrolase activity
GO:0016887 ATP hydrolysis activity
GO:0043138 3'-5' DNA helicase activity
GO:0043139 5'-3' DNA helicase activity
Biological Process
GO:0000492 box C/D snoRNP assembly
GO:0006281 DNA repair
GO:0006325 chromatin organization
GO:0006338 chromatin remodeling
GO:0006355 regulation of DNA-templated transcription
GO:0006357 regulation of transcription by RNA polymerase II
GO:0006364 rRNA processing
GO:0032508 DNA duplex unwinding
GO:0050821 protein stabilization
Cellular Component
GO:0000785 chromatin
GO:0000812 Swr1 complex
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0031011 Ino80 complex
GO:0035267 NuA4 histone acetyltransferase complex
GO:0097255 R2TP complex

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8euf, PDBe:8euf, PDBj:8euf
PDBsum8euf
PubMed37384669
UniProtQ12464|RUVB2_YEAST RuvB-like protein 2 (Gene Name=RVB2)

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