Structure of PDB 8kd4 Chain O Binding Site BS01

Receptor Information
>8kd4 Chain O (length=98) Species: 8355 (Xenopus laevis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQS
SAVMALQEASEAYLVALFEDTNLAAIHAKRVTIMPKDIQLARRIRGER
Ligand information
>8kd4 Chain X (length=164) [Search DNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
ggcggccgctctagaacaggatgtatatatctgacacgtgcctggagact
agggagtaatccccttggcggttaaaacgcgggggacagcgcgtacgtgc
gtttaagcggtgctagagctgtctacgaccaattgagcggcctcggcacc
gggattctccaggg
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB8kd4 Structural basis of nucleosome deacetylation and DNA linker tightening by Rpd3S histone deacetylase complex.
Resolution2.93 Å
Binding residue
(original residue number in PDB)		R40 Y41 P43 G44 V46 A47 R49 R53 R63 K64 L65 P66 R69 R83
Binding residue
(residue number reindexed from 1)		R4 Y5 P7 G8 V10 A11 R13 R17 R27 K28 L29 P30 R33 R47
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0005515 protein binding
GO:0030527 structural constituent of chromatin
GO:0046982 protein heterodimerization activity
Cellular Component
GO:0000786 nucleosome
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005694 chromosome

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:8kd4, PDBe:8kd4, PDBj:8kd4
PDBsum8kd4
PubMed37666978
UniProtP84233|H32_XENLA Histone H3.2

[Back to BioLiP]