6KMB | pdb_00006kmb

Crystal structure of Sth1 bromodomain

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d6kmbd_	All alpha proteins	Bromodomain-like	Bromodomain	automated matches	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
C	d6kmbc_	All alpha proteins	Bromodomain-like	Bromodomain	automated matches	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
B	d6kmbb_	All alpha proteins	Bromodomain-like	Bromodomain	automated matches	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
A	d6kmba_	All alpha proteins	Bromodomain-like	Bromodomain	automated matches	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	Dyp_perox_N	e6kmbD1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Dyp_perox_N	ECOD (v294.1)
C	Dyp_perox_N	e6kmbC1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Dyp_perox_N	ECOD (v294.1)
B	Dyp_perox_N	e6kmbB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Dyp_perox_N	ECOD (v294.1)
A	Dyp_perox_N	e6kmbA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Dyp_perox_N	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.20.920.10	Mainly Alpha	Up-down Bundle	Histone Acetyltransferase	Chain A	CATH (utative)
C	1.20.920.10	Mainly Alpha	Up-down Bundle	Histone Acetyltransferase	Chain A	CATH (utative)
B	1.20.920.10	Mainly Alpha	Up-down Bundle	Histone Acetyltransferase	Chain A	CATH (utative)
A	1.20.920.10	Mainly Alpha	Up-down Bundle	Histone Acetyltransferase	Chain A	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00439	Bromodomain (Bromodomain)	Bromodomain	Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Nuclear protein STH1/NPS1	nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on a nucleic acid helicase activity macromolecular conformation isomerase activity catalytic activity ATP-dependent activity protein binding binding histone binding histone H3K14ac reader activity histone reader activity histone H3 reader activity chromatin-protein adaptor activity nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on a nucleic acid helicase activity macromolecular conformation isomerase activity catalytic activity ATP-dependent activity protein binding binding histone binding histone H3K14ac reader activity histone reader activity histone H3 reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity chromatin binding histone H2A reader activity ATP-dependent activity, acting on DNA DNA helicase activity catalytic activity, acting on DNA ATP-dependent chromatin remodeler activity adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding histone H4 reader activity nucleosome array spacer activity histone octamer slider activity DNA translocase activity pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides	cellular process cell cycle chromosome segregation cell cycle process cellular component disassembly protein-containing complex organization protein-DNA complex disassembly protein-containing complex disassembly cellular component organization protein-DNA complex organization chromatin organization nucleosome disassembly chromatin remodeling cellular component organization or biogenesis cellular process cell cycle chromosome segregation cell cycle process cellular component disassembly protein-containing complex organization protein-DNA complex disassembly protein-containing complex disassembly cellular component organization protein-DNA complex organization chromatin organization nucleosome disassembly chromatin remodeling cellular component organization or biogenesis nucleosome organization organelle assembly chromosome organization membraneless organelle assembly CENP-A containing chromatin assembly cellular component biogenesis organelle organization cellular component assembly kinetochore assembly protein-containing complex assembly kinetochore organization cytoskeleton organization regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process cellular response to stimulus response to stimulus DNA metabolic process base-excision repair cellular response to stress DNA damage response response to stress DNA repair negative regulation of biological process negative regulation of cellular process negative regulation of macromolecule metabolic process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process heterochromatin organization negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic transcription elongation by RNA polymerase II DNA-templated transcription elongation transcription by RNA polymerase II double-strand break repair sexual reproduction reproductive process meiotic cell cycle positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process	RSC-type complex membrane-bounded organelle ATPase complex protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membraneless organelle chromatin chromosome intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure RSC-type complex membrane-bounded organelle ATPase complex protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membraneless organelle chromatin chromosome intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure organelle membraneless organelle SWI/SNF superfamily-type complex chromosome, centromeric region chromosomal region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR018359	Bromodomain, conserved site	Conserved Site
A, B, C, D	IPR001487	Bromodomain	Domain
A, B, C, D	IPR049730	SNF2/RAD5-like, C-terminal helicase domain	Domain
A, B, C, D	IPR038718	SNF2-like, N-terminal domain superfamily	Homologous Superfamily
A, B, C, D	IPR000330	SNF2, N-terminal domain	Domain
A, B, C, D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, C, D	IPR001650	Helicase, C-terminal domain-like	Domain
A, B, C, D	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A, B, C, D	IPR036427	Bromodomain-like superfamily	Homologous Superfamily
A, B, C, D	IPR014012	Helicase/SANT-associated domain	Domain
A, B, C, D	IPR029295	Snf2, ATP coupling domain	Domain

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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.