3VD1 | pdb_00003vd1

structure of p73 DNA binding domain tetramer modulates p73 transactivation

External Resource: Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d3vd1b1	All beta proteins	Common fold of diphtheria toxin/transcription factors/cytochrome f	p53-like transcription factors	p53 DNA-binding domain-like	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3vd1b2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3vd1c1	All beta proteins	Common fold of diphtheria toxin/transcription factors/cytochrome f	p53-like transcription factors	p53 DNA-binding domain-like	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3vd1c2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3vd1d1	All beta proteins	Common fold of diphtheria toxin/transcription factors/cytochrome f	p53-like transcription factors	p53 DNA-binding domain-like	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3vd1d2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth I]	d3vd1i1	All beta proteins	Common fold of diphtheria toxin/transcription factors/cytochrome f	p53-like transcription factors	p53 DNA-binding domain-like	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth I]	d3vd1i2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth J]	d3vd1j1	All beta proteins	Common fold of diphtheria toxin/transcription factors/cytochrome f	p53-like transcription factors	p53 DNA-binding domain-like	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth J]	d3vd1j2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G [auth K]	d3vd1k1	All beta proteins	Common fold of diphtheria toxin/transcription factors/cytochrome f	p53-like transcription factors	p53 DNA-binding domain-like	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G [auth K]	d3vd1k2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H [auth L]	d3vd1l1	All beta proteins	Common fold of diphtheria toxin/transcription factors/cytochrome f	p53-like transcription factors	p53 DNA-binding domain-like	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H [auth L]	d3vd1l2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3vd1a1	All beta proteins	Common fold of diphtheria toxin/transcription factors/cytochrome f	p53-like transcription factors	p53 DNA-binding domain-like	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3vd1a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	p53-like transcription factors	8070549	3000758	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	p53-like transcription factors	8070549	3000758	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	p53-like transcription factors	8070549	3000758	SCOP2B (2022-06-29)
E [auth I]	SCOP2B Superfamily	p53-like transcription factors	8070549	3000758	SCOP2B (2022-06-29)
F [auth J]	SCOP2B Superfamily	p53-like transcription factors	8070549	3000758	SCOP2B (2022-06-29)
G [auth K]	SCOP2B Superfamily	p53-like transcription factors	8070549	3000758	SCOP2B (2022-06-29)
H [auth L]	SCOP2B Superfamily	p53-like transcription factors	8070549	3000758	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	p53-like transcription factors	8070549	3000758	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)
B	P53	e3vd1B1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Common fold of diphtheria toxin/transcription factors/cytochrome f	F: P53	ECOD (1.6)
C	P53	e3vd1C1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Common fold of diphtheria toxin/transcription factors/cytochrome f	F: P53	ECOD (1.6)
D	P53	e3vd1D1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Common fold of diphtheria toxin/transcription factors/cytochrome f	F: P53	ECOD (1.6)
E [auth I]	P53	e3vd1I1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Common fold of diphtheria toxin/transcription factors/cytochrome f	F: P53	ECOD (1.6)
F [auth J]	P53	e3vd1J1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Common fold of diphtheria toxin/transcription factors/cytochrome f	F: P53	ECOD (1.6)
G [auth K]	P53	e3vd1K1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Common fold of diphtheria toxin/transcription factors/cytochrome f	F: P53	ECOD (1.6)
H [auth L]	P53	e3vd1L1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Common fold of diphtheria toxin/transcription factors/cytochrome f	F: P53	ECOD (1.6)
A	P53	e3vd1A1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Common fold of diphtheria toxin/transcription factors/cytochrome f	F: P53	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.60.40.720	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
C	2.60.40.720	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
D	2.60.40.720	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
E [auth I]	2.60.40.720	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
F [auth J]	2.60.40.720	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
G [auth K]	2.60.40.720	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
H [auth L]	2.60.40.720	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
A	2.60.40.720	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E [auth I], A, B, C, D, E [auth I], F [auth J], G [auth K], H [auth L]	PF00870	P53 DNA-binding domain (P53)	P53 DNA-binding domain	This family contains one anomalous member, viz: Zea mays (Q6JAD8). This sequence is identical to human P53 and would appear to be a a human contaminant within the Zea mays sampling effort.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E [auth I], A, B, C, D, E [auth I], F [auth J], G [auth K], H [auth L]	Tumor protein p73	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity cation binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity cation binding ion binding metal ion binding small molecule binding identical protein binding protein binding p53 binding transcription factor binding transcription coregulator binding transcription corepressor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding RNA polymerase II cis-regulatory region sequence-specific DNA binding MDM2/MDM4 family protein binding kinase binding enzyme binding protein kinase binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process multicellular organismal process regulation of cellular process regulation of developmental process cellular developmental process negative regulation of biological process regulation of cell differentiation neurogenesis multicellular organism development cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process multicellular organismal process regulation of cellular process regulation of developmental process cellular developmental process negative regulation of biological process regulation of cell differentiation neurogenesis multicellular organism development neuron differentiation cell differentiation negative regulation of cellular process anatomical structure development negative regulation of cell differentiation system development developmental process regulation of biological process negative regulation of developmental process biological regulation nervous system development generation of neurons negative regulation of neuron differentiation regulation of neuron differentiation response to chemical response to xenobiotic stimulus regulation of body fluid levels secretion by tissue secretion transport cerebrospinal fluid secretion establishment of localization body fluid secretion localization regulation of biological quality cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein tetramerization protein-containing complex assembly cellular component organization or biogenesis mismatch repair primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process metabolic process macromolecule metabolic process DNA repair regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process regulation of growth regulation of cardiac muscle tissue growth developmental growth cardiac muscle cell proliferation negative regulation of cardiac muscle tissue growth organ growth striated muscle tissue development negative regulation of organ growth negative regulation of growth regulation of organ growth regulation of heart growth regulation of cardiac muscle cell proliferation muscle cell proliferation regulation of multicellular organismal process cardiac muscle tissue growth muscle tissue development striated muscle cell proliferation heart development negative regulation of cell population proliferation heart growth regulation of multicellular organismal development cell population proliferation regulation of developmental growth negative regulation of heart growth cardiac muscle tissue development growth animal organ development tissue development circulatory system development negative regulation of developmental growth regulation of cell population proliferation negative regulation of multicellular organismal process negative regulation of cardiac muscle cell proliferation positive regulation of cell communication positive regulation of signal transduction regulation of cellular response to stress positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator regulation of signal transduction regulation of intrinsic apoptotic signaling pathway in response to DNA damage regulation of programmed cell death intracellular signal transduction regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator cell communication intrinsic apoptotic signaling pathway in response to DNA damage signal transduction intrinsic apoptotic signaling pathway positive regulation of programmed cell death positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage regulation of apoptotic process positive regulation of intracellular signal transduction cell death positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator regulation of response to stimulus intrinsic apoptotic signaling pathway by p53 class mediator regulation of apoptotic signaling pathway signaling positive regulation of biological process regulation of intrinsic apoptotic signaling pathway positive regulation of apoptotic signaling pathway intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator positive regulation of response to stimulus regulation of intracellular signal transduction regulation of response to stress regulation of signal transduction by p53 class mediator positive regulation of signal transduction by p53 class mediator positive regulation of cellular process regulation of signaling signal transduction by p53 class mediator positive regulation of apoptotic process apoptotic signaling pathway regulation of cell communication positive regulation of intrinsic apoptotic signaling pathway apoptotic process regulation of intrinsic apoptotic signaling pathway by p53 class mediator programmed cell death positive regulation of signaling digestive system development tube development digestive tract development anatomical structure morphogenesis tube morphogenesis digestive tract morphogenesis respiratory tube development positive regulation of lung ciliated cell differentiation epithelial cell differentiation regulation of epithelial cell differentiation positive regulation of developmental process positive regulation of cell differentiation lung development respiratory system development epithelium development lung ciliated cell differentiation regulation of lung ciliated cell differentiation lung epithelium development positive regulation of epithelial cell differentiation multi-ciliated epithelial cell differentiation lung epithelial cell differentiation lung cell differentiation positive regulation of multicellular organismal process columnar/cuboidal epithelial cell differentiation kidney development renal system development positive regulation of DNA-templated transcription RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription head development forebrain development brain development pallium development central nervous system development telencephalon development hippocampus development limbic system development regulation of mitotic cell cycle cell cycle regulation of cell cycle mitotic cell cycle neuron apoptotic process negative regulation of neuron apoptotic process negative regulation of programmed cell death negative regulation of apoptotic process regulation of neuron apoptotic process intracellular signaling cassette positive regulation of MAPK cascade regulation of MAPK cascade MAPK cascade defense response inflammatory response positive regulation of cell size regulation of cellular component size regulation of cell size regulation of anatomical structure size positive regulation of nervous system development cell development regulation of neurogenesis regulation of gliogenesis positive regulation of gliogenesis regulation of cell development regulation of nervous system development gliogenesis positive regulation of neurogenesis positive regulation of oligodendrocyte differentiation positive regulation of cell development regulation of glial cell differentiation positive regulation of glial cell differentiation oligodendrocyte differentiation glial cell differentiation regulation of oligodendrocyte differentiation apoptotic mitochondrial changes release of cytochrome c from mitochondria organelle organization mitochondrion organization post-embryonic development neuron development	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle Golgi apparatus intracellular membrane-bounded organelle endomembrane system cellular anatomical structure intracellular anatomical structure cytoplasm cytosol intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle Golgi apparatus intracellular membrane-bounded organelle endomembrane system cilium plasma membrane bounded cell projection ciliary basal body cell projection microtubule organizing center cytoskeleton microtubule cytoskeleton cell junction centrosome cell periphery plasma membrane membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
I [auth E], J [auth F], K [auth G], L [auth H], M, I [auth E], J [auth F], K [auth G], L [auth H], M, N, O, P	DNA (5'-D(CPGPGPGPCPAPTPGPCPCPCPG)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E [auth I], A, B, C, D, E [auth I], F [auth J], G [auth K], H [auth L]	IPR012346	p53/RUNT-type transcription factor, DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D, E [auth I], A, B, C, D, E [auth I], F [auth J], G [auth K], H [auth L]	IPR036674	p53-like tetramerisation domain superfamily	Homologous Superfamily
A, B, C, D, E [auth I], A, B, C, D, E [auth I], F [auth J], G [auth K], H [auth L]	IPR011615	p53, DNA-binding domain	Domain
A, B, C, D, E [auth I], A, B, C, D, E [auth I], F [auth J], G [auth K], H [auth L]	IPR001660	Sterile alpha motif domain	Domain
A, B, C, D, E [auth I], A, B, C, D, E [auth I], F [auth J], G [auth K], H [auth L]	IPR002117	p53 tumour suppressor family	Family
A, B, C, D, E [auth I], A, B, C, D, E [auth I], F [auth J], G [auth K], H [auth L]	IPR037612	Tumour protein p73, SAM domain	Domain
A, B, C, D, E [auth I], A, B, C, D, E [auth I], F [auth J], G [auth K], H [auth L]	IPR008967	p53-like transcription factor, DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D, E [auth I], A, B, C, D, E [auth I], F [auth J], G [auth K], H [auth L]	IPR010991	p53, tetramerisation domain	Domain
A, B, C, D, E [auth I], A, B, C, D, E [auth I], F [auth J], G [auth K], H [auth L]	IPR013761	Sterile alpha motif/pointed domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E [auth I], A, B, C, D, E [auth I], F [auth J], G [auth K], H [auth L]	Pharos: O15350	adult T-cell leukemia/lymphoma Inflammation small cell lung carcinoma breast carcinoma alveolar rhabdomyosarcoma acute T cell leukemia breast cancer primary ciliary dyskinesia lissencephaly spectrum disorders malignant ependymoma small cell carcinoma cancer lung benign neoplasm

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.