Structure of PDB 8kcc Chain K Binding Site BS03

Receptor Information
>8kcc Chain K (length=508) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EETVIKLQNELCPLLTGGQLKSYQLKGVKWLISLWQNGLNGILADQMGLG
KTIQTIGFLSHLKGNGLDGPYLVIAPLSTLSNWFNEIARFTPSINAIIYH
GDKNQRDELRRKHMPKTVGPKFPIVITSYEVAMNDAKRILRHYPWKYVVI
DEGHRLKNHKCKLLRELKHLKMDNKLLLTGTPLQNNLSELWSLLNFILPD
IFTSHDEFESWFEKRRAQVVSKLHGILRPFILRRMKCDVELSLPRKKEII
MYATMTDHQKKFQEHLVNNTLEAHLNLVIQLRKNCNHPDLLQGQIDGSYL
YPPVEEIVGQCGKFRLLERLLVRLFANNHKVLIFSQWTKLLDIMDYYFSE
KGFEVCRIDGSVKLDERRRQIKDFSDEKSSCSIFLLSTRAGGLGINLTAA
DTCILYDSDWNPQMDLQAMDRCHRIGQTKPVHVYRLSTAQSIETRVLKRA
YSKLKLEHVVEDKLIQTDISDADLDRLLDRSDLTFPVKGPGWEVVLPSSG
GMLSSLNS
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 chain8kcc 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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PDB8kcc Mechanism of heterochromatin remodeling revealed by the DDM1 bound nucleosome structures.
Resolution3.1 Å
Binding residue
(original residue number in PDB)		Q201 Q206 L231 G232 K233 T234 I235 N608 R636 I637
Binding residue
(residue number reindexed from 1)		Q19 Q24 L49 G50 K51 T52 I53 N396 R424 I425
Annotation score5
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
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:8kcc, PDBe:8kcc, PDBj:8kcc
PDBsum8kcc
PubMed38870940
UniProtQ9XFH4|DDM1_ARATH ATP-dependent DNA helicase DDM1 (Gene Name=DDM1)

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