3RQD

Ideal Thiolate-Zinc Coordination Geometry in Depsipeptide Binding to Histone Deacetylase 8

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Arginase/deacetylase-like	8040016	3000260	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Arginase/deacetylase-like	8040016	3000260	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF00850	e3rqdA1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Arginase/deacetylase	F: PF00850	ECOD (1.6)
B	PF00850	e3rqdB1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Arginase/deacetylase	F: PF00850	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.800.20	Alpha Beta	3-Layer(aba) Sandwich	Arginase	Chain A	CATH (4.3.0)
B	3.40.800.20	Alpha Beta	3-Layer(aba) Sandwich	Arginase	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00850	Histone deacetylase domain (Hist_deacetyl)	Histone deacetylase domain	Histones can be reversibly acetylated on several lysine residues. Regulation of transcription is caused in part by this mechanism. Histone deacetylases catalyse the removal of the acetyl group. Histone deacetylases are related to other proteins [1]. ...	Histones can be reversibly acetylated on several lysine residues. Regulation of transcription is caused in part by this mechanism. Histone deacetylases catalyse the removal of the acetyl group. Histone deacetylases are related to other proteins [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Histone deacetylase 8	Hsp90 protein binding protein binding binding heat shock protein binding catalytic activity, acting on a protein hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity histone modifying activity protein decrotonylase activity catalytic activity histone decrotonylase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds transcription factor binding DNA-binding transcription factor binding Hsp90 protein binding protein binding binding heat shock protein binding catalytic activity, acting on a protein hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity histone modifying activity protein decrotonylase activity catalytic activity histone decrotonylase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds transcription factor binding DNA-binding transcription factor binding Hsp70 protein binding protein-folding chaperone binding deacetylase activity protein lysine deacetylase activity cation binding ion binding metal ion binding small molecule binding histone deacetylase activity	regulation of protein stability biological regulation regulation of biological quality cellular component organization organelle organization mitotic sister chromatid cohesion chromosome organization sister chromatid cohesion cellular process cellular component organization or biogenesis cell cycle cell cycle process negative regulation of post-translational protein modification regulation of protein modification process regulation of protein stability biological regulation regulation of biological quality cellular component organization organelle organization mitotic sister chromatid cohesion chromosome organization sister chromatid cohesion cellular process cellular component organization or biogenesis cell cycle cell cycle process negative regulation of post-translational protein modification regulation of protein modification process negative regulation of biological process regulation of protein ubiquitination regulation of primary metabolic process organic substance metabolic process protein ubiquitination negative regulation of protein modification process protein metabolic process negative regulation of protein ubiquitination regulation of protein modification by small protein conjugation or removal protein modification process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biological process organonitrogen compound metabolic process negative regulation of protein modification by small protein conjugation or removal regulation of post-translational protein modification regulation of protein metabolic process negative regulation of metabolic process primary metabolic process regulation of macromolecule metabolic process macromolecule modification metabolic process macromolecule metabolic process post-translational protein modification regulation of metabolic process protein modification by small protein conjugation protein modification by small protein conjugation or removal regulation of cellular process negative regulation of cellular metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II cellular metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process negative regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process regulation of telomere maintenance regulation of cellular component organization telomere organization regulation of chromosome organization DNA metabolic process regulation of organelle organization telomere maintenance regulation of DNA metabolic process protein-DNA complex organization protein-containing complex organization chromatin organization	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen nuclear chromosome chromosome intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen nuclear chromosome chromosome intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle protein-containing complex catalytic complex nuclear protein-containing complex histone deacetylase complex nucleoplasm cytoplasm
C, D	Largazole	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR000286	Histone deacetylase family	Family
A, B	IPR003084	Histone deacetylase	Family
A, B	IPR023801	Histone deacetylase domain	Domain
A, B	IPR037138	Histone deacetylase domain superfamily	Homologous Superfamily
A, B	IPR023696	Ureohydrolase domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q9BY41	Cornelia de Lange syndrome Cornelia de Lange syndrome 5 intellectual disability Wilson-Turner syndrome acquired metabolic disease osteosarcoma plasma cell myeloma Radial club hand mature T-cell and NK-cell non-Hodgkin lymphoma pancreatic intraductal papillary-mucinous neoplasm primary cutaneous T-cell lymphoma obesity disorder pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C, D	02G
C, D	03Y	Parent Component: CYS
C, D	BB9	Parent Component: CYS RESID: AA0241 , AA0242 , AA0243 , AA0244 , AA0466 , AA0467 , AA0485 , AA0541 PSI-MOD : glycine thiazole-4-carboxylic acid MOD:00246 , L-serine thiazole-4-carboxylic acid MOD:00247 , L-phenylalanine thiazole-4-carboxylic acid MOD:00248 , L-cysteine thiazole-4-carboxylic acid MOD:00249 , L-isoleucine thiazole-4-carboxylic acid MOD:01389 , L-valine thiazole-4-carboxylic acid MOD:01390 , L-threonine thiazoline-4-carboxylic acid MOD:01408 , L-glutamate thiazole-4-carboxylic acid MOD:01815

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.