Structure of PDB 8wh8 Chain K Binding Site BS03

Receptor Information
>8wh8 Chain K (length=443) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KSYQLKGVKWLISLWQNGLNGILADQMGLGKTIQTIGFLSHLKGNGLDGP
YLVIAPLSTLSNWFNEIARFTPSINAIIYHGDKNQRDELRRKHMPKTVGP
KFPIVITSYEVAMNDAKRILRHYPWKYVVIDEGHRLKNHKCKLLRELKHL
KMDNKLLLTGTPLQNNLSELWSLLNFILPDIQVVSKLHGILRPFILRRMK
CDVELSLPRKKEIIMYATMTDHQKKFQEHLVNNTLEAHLGENAIRGQGWK
GKLNNLVIQLRKNCNHPDLLQGQIDGSYLYPPVEEIVGQCGKFRLLERLL
VRLFANNHKVLIFSQWTKLLDIMDYYFSEKGFEVCRIDGSVKLDERRRQI
KDFSDEKSSCSIFLLSTRAGGLGINLTAADTCILYDSDWNPQMDLQAMDR
CHRIGQTKPVHVYRLSTAQSIETRVLKRAYSKLKLEHVVIGQG
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 chain8wh8 Chain K Residue 801 [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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PDB8wh8 Molecular basis of chromatin remodelling by DDM1 involved in plant DNA methylation.
Resolution3.6 Å
Binding residue
(original residue number in PDB)		K203 Y205 G232 I235 F272 V436
Binding residue
(residue number reindexed from 1)		K1 Y3 G30 I33 F70 V203
Annotation score5
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:0004386 helicase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016787 hydrolase activity
GO:0016887 ATP hydrolysis activity
GO:0140658 ATP-dependent chromatin remodeler activity
Biological Process
GO:0006338 chromatin remodeling
GO:0006346 DNA methylation-dependent heterochromatin formation
GO:0009294 DNA-mediated transformation
GO:0031507 heterochromatin formation
GO:0032197 retrotransposition
GO:0032508 DNA duplex unwinding
GO:0040029 epigenetic regulation of gene expression
Cellular Component
GO:0000786 nucleosome
GO:0005634 nucleus

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8wh8, PDBe:8wh8, PDBj:8wh8
PDBsum8wh8
PubMed38413824
UniProtQ9XFH4|DDM1_ARATH ATP-dependent DNA helicase DDM1 (Gene Name=DDM1)

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