7RJL | pdb_00007rjl

Crystal structure of human Bromodomain containing protein 3 (BRD3) in complex with SHMT

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	RF-1	e7rjlB1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: RF-1	ECOD (v294.1)
A	RF-1	e7rjlA1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: RF-1	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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
C, D	Serine hydroxymethyltransferase, cytosolic	threonine aldolase activity lyase activity catalytic activity carbon-carbon lyase activity aldehyde-lyase activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding cation binding threonine aldolase activity lyase activity catalytic activity carbon-carbon lyase activity aldehyde-lyase activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding cation binding organic acid binding serine binding amino acid binding carboxylic acid binding translation regulator activity mRNA regulatory element binding translation repressor activity translation repressor activity identical protein binding protein binding protein homodimerization activity protein dimerization activity transferase activity, transferring one-carbon groups glycine hydroxymethyltransferase activity transferase activity hydroxymethyl-, formyl- and related transferase activity hydroxytrimethyllysine aldolase activity molecular adaptor activity RNA binding mRNA 5'-UTR binding nucleic acid binding mRNA binding lamin binding	regulation of cellular process negative regulation of biological process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process negative regulation of metabolic process regulation of cellular process negative regulation of biological process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process regulation of translation negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process pyrimidine deoxyribonucleotide metabolic process deoxyribose phosphate biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process pyrimidine nucleotide metabolic process pyrimidine deoxyribonucleoside monophosphate metabolic process nucleobase-containing compound metabolic process pyrimidine deoxyribonucleotide biosynthetic process nucleobase-containing small molecule metabolic process dTMP metabolic process phosphate-containing compound metabolic process deoxyribonucleoside monophosphate biosynthetic process dTMP biosynthetic process small molecule metabolic process pyrimidine deoxyribonucleoside monophosphate biosynthetic process pyrimidine-containing compound biosynthetic process nucleoside monophosphate metabolic process phosphorus metabolic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process pyrimidine nucleoside monophosphate metabolic process pyrimidine-containing compound metabolic process 2'-deoxyribonucleotide metabolic process 2'-deoxyribonucleotide biosynthetic process nucleotide metabolic process nucleobase-containing compound biosynthetic process nucleoside monophosphate biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process pyrimidine nucleoside monophosphate biosynthetic process pyrimidine nucleotide biosynthetic process protein-containing complex organization protein homotetramerization cellular component organization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly protein homooligomerization cellular component organization or biogenesis nucleobase biosynthetic process purine nucleobase metabolic process purine nucleobase biosynthetic process purine-containing compound metabolic process purine-containing compound biosynthetic process nucleobase metabolic process folic acid-containing compound metabolic process tetrahydrofolate interconversion modified amino acid metabolic process tetrahydrofolate metabolic process pteridine-containing compound metabolic process one-carbon metabolic process catabolic process oxoacid metabolic process L-amino acid catabolic process carboxylic acid metabolic process amino acid metabolic process organic acid catabolic process organic acid metabolic process L-serine catabolic process alpha-amino acid metabolic process L-serine metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process carboxylic acid catabolic process small molecule catabolic process amino acid catabolic process glycine metabolic process carnitine metabolic process amino-acid betaine biosynthetic process carnitine biosynthetic process modified amino acid biosynthetic process amino-acid betaine metabolic process dicarboxylic acid metabolic process folic acid metabolic process response to peptide response to stimulus response to chemical response to cytokine response to leukemia inhibitory factor cellular response to cytokine stimulus cellular response to leukemia inhibitory factor cellular response to nitrogen compound cellular response to stimulus response to tetrahydrofolate cellular response to tetrahydrofolate response to oxygen-containing compound response to nitrogen compound cellular response to oxygen-containing compound cellular response to chemical stimulus	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle extracellular exosome extracellular vesicle extracellular organelle extracellular region vesicle extracellular membrane-bounded organelle membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle extracellular exosome extracellular vesicle extracellular organelle extracellular region vesicle extracellular membrane-bounded organelle cytosol nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
A, B	Bromodomain-containing protein 3	histone H3K9me2/3 reader activity histone reader activity histone H3 reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity protein binding binding histone binding RNA binding lncRNA binding nucleic acid binding chromatin binding histone H3K18cr reader activity histone H3K9me2/3 reader activity histone reader activity histone H3 reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity protein binding binding histone binding RNA binding lncRNA binding nucleic acid binding chromatin binding histone H3K18cr reader activity molecular condensate scaffold activity histone H3K27cr reader activity histone H3K9cr reader activity protein serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups	developmental process multicellular organismal process formation of primary germ layer cellular developmental process embryonic morphogenesis tissue development embryo development gastrulation anatomical structure morphogenesis multicellular organism development endoderm development cell differentiation anatomical structure development anatomical structure formation involved in morphogenesis developmental process multicellular organismal process formation of primary germ layer cellular developmental process embryonic morphogenesis tissue development embryo development gastrulation anatomical structure morphogenesis multicellular organism development endoderm development cell differentiation anatomical structure development anatomical structure formation involved in morphogenesis cellular process endoderm formation endodermal cell differentiation localization protein localization to chromatin protein localization to chromosome protein localization to organelle macromolecule localization intracellular protein localization 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 transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II 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 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 positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR019798	Serine hydroxymethyltransferase, pyridoxal phosphate binding site	Binding Site
C, D	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
C, D	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
C, D	IPR039429	Serine hydroxymethyltransferase-like domain	Domain
C, D	IPR001085	Serine hydroxymethyltransferase	Family
C, D	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
C, D	IPR049943	Serine hydroxymethyltransferase-like	Family
A, B	IPR043508	Brdt, bromodomain, repeat I	Domain
A, B	IPR027353	NET domain	Domain
A, B	IPR043509	Brdt, bromodomain, repeat II	Domain
A, B	IPR018359	Bromodomain, conserved site	Conserved Site
A, B	IPR001487	Bromodomain	Domain
A, B	IPR050935	Bromodomain-containing chromatin reader	Family
A, B	IPR038336	NET domain superfamily	Homologous Superfamily
A, B	IPR036427	Bromodomain-like superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, D	Pharos: P34896	nervous system disorder breast carcinoma Lymphoma, Small Noncleaved-Cell nephrosclerosis pancreatic ductal adenocarcinoma reticulum cell sarcoma atypical teratoid rhabdoid tumor psoriasis schizophrenia breast cancer ductal breast carcinoma in situ invasive ductal breast carcinoma lung adenocarcinoma lymphosarcoma non-Hodgkin lymphoma nervous system disorder breast carcinoma Lymphoma, Small Noncleaved-Cell nephrosclerosis pancreatic ductal adenocarcinoma reticulum cell sarcoma atypical teratoid rhabdoid tumor psoriasis schizophrenia breast cancer ductal breast carcinoma in situ invasive ductal breast carcinoma lung adenocarcinoma lymphosarcoma non-Hodgkin lymphoma attention deficit hyperactivity disorder, inattentive type esophageal adenocarcinoma large cell medulloblastoma
A, B	Pharos: Q15059	medulloblastoma adult medulloblastoma medullomyoblastoma with myogenic differentiation childhood medulloblastoma melanotic medulloblastoma Conventional (Clear Cell) Renal Cell Carcinoma osteosarcoma subependymal giant cell astrocytoma astrocytic tumor desmoplastic/nodular medulloblastoma ovarian cancer gastric adenocarcinoma pancreatic ductal adenocarcinoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C, D	ALY	Parent Component: LYS RESID: AA0055 PSI-MOD : N6-acetyl-L-lysine MOD:00064

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.

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