Structure of PDB 8kcb Chain K Binding Site BS04

Receptor Information
>8kcb Chain K (length=486) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ETVIKLQNELCPLLTGGQLKSYQLKGVKWLISLWQNGLNGILADQMGLGK
TIQTIGFLSHLKGNGLDGPYLVIAPLSTLSNWFNEIARFTPSINAIIYHG
DKNQRDELRRKHMPKTVGPKFPIVITSYEVAMNDAKRILRHYPWKYVVID
EGHRLKNHKCKLLRELKHLKMDNKLLLTGTPLQNNLSELWSLLNFILPDI
FTSHDEFESWFEKRRAQVVSKLHGILRPFILRRMKCDVELSLPRKKEIIM
YATMTDHQKKFQEHLLVIQLRKNCNHPDLLQGQIDGSYLYPPVEEIVGQC
GKFRLLERLLVRLFANNHKVLIFSQWTKLLDIMDYYFSEKGFEVCRIDGS
VKLDERRRQIKDFSDEKSSCSIFLLSTRAGGLGINLTAADTCILYDSDWN
PQMDLQAMDRCHRIGQTKPVHVYRLSTAQSIETRVLKRAYSKLKLEHVVE
DKLIQTDISDADLDRLLDRSDLTFPVKGPGWEVVLP
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 chain8kcb Chain K Residue 902 [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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PDB8kcb Mechanism of heterochromatin remodeling revealed by the DDM1 bound nucleosome structures.
Resolution3.17 Å
Binding residue
(original residue number in PDB)		Q206 M229 G232 T234 I235 N608 R636 I637
Binding residue
(residue number reindexed from 1)		Q23 M46 G49 T51 I52 N385 R413 I414
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8kcb, PDBe:8kcb, PDBj:8kcb
PDBsum8kcb
PubMed38870940
UniProtQ9XFH4|DDM1_ARATH ATP-dependent DNA helicase DDM1 (Gene Name=DDM1)

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