5T8R | pdb_00005t8r

Crystal structure of human BAZ2A PHD zinc finger in complex with unmodified H3 10-mer

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	FYVE/PHD zinc finger	8084746	3001459	SCOP2B (2022-06-29)
C	SCOP2 Family	PHD domain	8084745	4003778	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	FYVE/PHD zinc finger	8084746	3001459	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	FYVE/PHD zinc finger	8084746	3001459	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	FYVE/PHD zinc finger	8084746	3001459	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)
D	DNAG_N	e5t8rD1	A: a/b three-layered sandwiches	X: Spectrin repeat-like	H: Spectrin repeat	T: Spectrin repeat	F: DNAG_N	ECOD (v294.1)
C	DNAG_N	e5t8rC1	A: a/b three-layered sandwiches	X: Spectrin repeat-like	H: Spectrin repeat	T: Spectrin repeat	F: DNAG_N	ECOD (v294.1)
B	DNAG_N	e5t8rB1	A: a/b three-layered sandwiches	X: Spectrin repeat-like	H: Spectrin repeat	T: Spectrin repeat	F: DNAG_N	ECOD (v294.1)
A	DNAG_N	e5t8rA1	A: a/b three-layered sandwiches	X: Spectrin repeat-like	H: Spectrin repeat	T: Spectrin repeat	F: DNAG_N	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)
C	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)
B	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)
A	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00628	PHD-finger (PHD)	PHD-finger	PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains [2]. Several PHD fingers have been identified as binding modules of methylated histone H3 [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E, F [auth G]	Histone H3.1	DNA binding binding nucleic acid binding cell adhesion molecule binding cadherin binding protein binding protein heterodimerization activity protein dimerization activity structural molecule activity structural constituent of chromatin	protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization organelle organization protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization organelle organization telomere organization chromosome organization regulation of biosynthetic process regulation of biological process regulation of cellular process epigenetic regulation of gene expression biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process	cellular anatomical structure membrane extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome cellular anatomical structure membrane extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome intracellular membraneless organelle chromatin chromosome intracellular organelle membraneless organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
A, B, C, D	Bromodomain adjacent to zinc finger domain protein 2A	protein binding binding histone binding histone H4K16ac reader activity histone reader activity histone H4 reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity RNA binding nucleic acid binding DNA binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding protein binding binding histone binding histone H4K16ac reader activity histone reader activity histone H4 reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity RNA binding nucleic acid binding DNA binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding DNA-binding transcription factor binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of cellular process negative regulation of biological process cellular component organization cellular component biogenesis cellular component assembly chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process biological regulation heterochromatin organization regulation of macromolecule metabolic process regulation of gene expression negative regulation of gene expression constitutive heterochromatin formation negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process DNA methylation-dependent constitutive heterochromatin formation negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process regulation of metabolic process regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of DNA-templated transcription transcription preinitiation complex assembly RNA polymerase I preinitiation complex assembly protein-DNA complex organization transcription initiation at RNA polymerase I promoter transcription by RNA polymerase I protein-containing complex assembly protein-containing complex organization protein-DNA complex assembly DNA-templated transcription initiation nucleolar chromatin organization rDNA heterochromatin formation nucleus organization organelle organization nucleolus organization facultative heterochromatin formation negative regulation of RNA biosynthetic process negative regulation of transcription by RNA polymerase I negative regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of transcription by RNA polymerase I negative regulation of RNA metabolic process	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen nuclear speck ribonucleoprotein granule nuclear body nucleoplasm supramolecular complex nuclear ribonucleoprotein granule cytoplasm cytosol ATPase complex protein-containing complex catalytic complex nuclear protein-containing complex chromatin chromosome ISWI-type complex SWI/SNF superfamily-type complex NoRC complex chromatin silencing complex rDNA heterochromatin heterochromatin

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E, F [auth G]	IPR009072	Histone-fold	Homologous Superfamily
E, F [auth G]	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
E, F [auth G]	IPR000164	Histone H3/CENP-A	Family
A, B, C, D	IPR001965	Zinc finger, PHD-type	Domain
A, B, C, D	IPR037374	BAZ2A/BAZ2B, bromodomain	Domain
A, B, C, D	IPR018359	Bromodomain, conserved site	Conserved Site
A, B, C, D	IPR028941	WHIM2 domain	Domain
A, B, C, D	IPR001487	Bromodomain	Domain
A, B, C, D	IPR018501	DDT domain	Domain
A, B, C, D	IPR019787	Zinc finger, PHD-finger	Domain
A, B, C, D	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A, B, C, D	IPR028940	Bromodomain adjacent to zinc finger domain protein 2A, PHD zinc finger	Domain
A, B, C, D	IPR016177	DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR028942	WHIM1 domain	Domain
A, B, C, D	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, B, C, D	IPR001739	Methyl-CpG DNA binding	Domain
A, B, C, D	IPR036427	Bromodomain-like superfamily	Homologous Superfamily
A, B, C, D	IPR017956	AT hook, DNA-binding motif	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E, F [auth G]	Pharos: P68431	lung carcinoma glioblastoma glioma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma allergic rhinitis ovarian cancer autism spectrum disorder psoriasis cutaneous lupus erythematosus tuberculosis ependymoma gastric carcinoma Glioma of Brain, Familial lung carcinoma glioblastoma glioma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma allergic rhinitis ovarian cancer autism spectrum disorder psoriasis cutaneous lupus erythematosus tuberculosis ependymoma gastric carcinoma Glioma of Brain, Familial hypertensive disorder lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm osteoarthritis astrocytoma (excluding glioblastoma) pancreatic intraductal papillary-mucinous carcinoma breast cancer spina bifida cystic fibrosis exocrine pancreatic carcinoma glioma susceptibility 1 invasive ductal breast carcinoma lung cancer malignant glioma medulloblastoma osteosarcoma atypical teratoid rhabdoid tumor pancreatic intraductal papillary-mucinous neoplasm breast carcinoma subependymoma ductal breast carcinoma in situ gastric cancer hepatocellular carcinoma
A, B, C, D	Pharos: Q9UIF9	prostate cancer acute myeloid leukemia malignant mesothelioma Prostatic Neoplasms atrial fibrillation osteosarcoma psoriasis lung cancer

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.