3QYM | pdb_00003qym

Structure of p63 DNA Binding Domain in Complex with a 10 Base Pair A/T Rich Response Element Half Site

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)
H	SCOP2B Superfamily	p53-like transcription factors	8070547	3000758	SCOP2B (2022-06-29)
G	SCOP2 Family	p53 DNA-binding domain-like	8070546	4001847	SCOP2 (2022-06-29)
G	SCOP2 Superfamily	p53-like transcription factors	8070547	3000758	SCOP2 (2022-06-29)
F	SCOP2B Superfamily	p53-like transcription factors	8070547	3000758	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	p53-like transcription factors	8070547	3000758	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	p53-like transcription factors	8070547	3000758	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	p53-like transcription factors	8070547	3000758	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	p53-like transcription factors	8070547	3000758	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	p53-like transcription factors	8070547	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)
H	P53	e3qymH1	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	P53	e3qymG1	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	P53	e3qymF1	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	P53	e3qymE1	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	e3qymD1	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	e3qymC1	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)
B	P53	e3qymB1	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	e3qymA1	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)
H	2.60.40.720	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
G	2.60.40.720	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
F	2.60.40.720	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
E	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)
C	2.60.40.720	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
B	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 A, B, C, D, E, F, G, H	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
I, J, K, L, M I, J, K, L, M, N, O, P	5'-D(APAPAPCPAPTPGPTPTPT)-3'	-	-	-
A, B, C, D, E A, B, C, D, E, F, G, H	Tumor protein 63	protein binding binding WW domain binding protein domain specific binding chromatin binding promoter-specific chromatin binding DNA binding 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 protein binding binding WW domain binding protein domain specific binding chromatin binding promoter-specific chromatin binding DNA binding 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 p53 binding sequence-specific DNA binding double-stranded DNA binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding MDM2/MDM4 family protein binding damaged DNA binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation multicellular organismal process limb development appendage development embryonic forelimb morphogenesis embryonic limb morphogenesis embryonic morphogenesis embryonic appendage morphogenesis embryo development multicellular organism development anatomical structure morphogenesis forelimb morphogenesis appendage morphogenesis anatomical structure development limb morphogenesis positive regulation of cell communication regulation of cellular process positive regulation of signal transduction signaling positive regulation of biological process regulation of signal transduction regulation of programmed cell death positive regulation of apoptotic signaling pathway cell communication positive regulation of response to stimulus signal transduction positive regulation of cellular process regulation of biological process regulation of signaling positive regulation of programmed cell death regulation of apoptotic process biological regulation cell death positive regulation of apoptotic process apoptotic signaling pathway regulation of response to stimulus regulation of cell communication apoptotic process programmed cell death positive regulation of signaling regulation of apoptotic signaling pathway epidermal cell division cell division regulation of epidermal cell division regulation of cell division negative regulation of mesoderm development regulation of developmental process negative regulation of developmental process negative regulation of biological process regulation of mesoderm development tissue development mesoderm development 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 skeletal system development system development establishment of skin barrier epithelium development skin development skin epidermis development epidermis development animal organ development cell-cell signaling ectoderm and mesoderm interaction cell population proliferation epithelial cell proliferation keratinocyte proliferation genitalia development reproductive system development sex differentiation female genitalia development female sex differentiation reproductive structure development animal organ morphogenesis genitalia morphogenesis female genitalia morphogenesis sympathetic nervous system development autonomic nervous system development nervous system development molting cycle process hair cycle epidermis morphogenesis morphogenesis of an epithelium tissue morphogenesis hair follicle development molting cycle hair cycle process hair follicle morphogenesis regulation of stem cell proliferation positive regulation of cell population proliferation positive regulation of stem cell proliferation stem cell proliferation regulation of cell population proliferation embryonic hindlimb morphogenesis hindlimb morphogenesis cellular developmental process prostate gland development gland development epithelial cell differentiation prostate glandular acinus development cell differentiation epithelial cell differentiation involved in prostate gland development squamous basal epithelial stem cell differentiation involved in prostate gland acinus development urogenital system development glandular epithelial cell differentiation stem cell differentiation columnar/cuboidal epithelial cell differentiation cellular senescence post-anal tail morphogenesis fibroblast apoptotic process positive regulation of fibroblast apoptotic process regulation of fibroblast apoptotic process lateral sprouting from an epithelium prostate gland epithelium morphogenesis gland morphogenesis morphogenesis of an epithelial bud animal organ formation morphogenesis of an epithelial fold morphogenesis of embryonic epithelium prostatic bud formation prostate gland morphogenesis morphogenesis of a branching structure anatomical structure formation involved in morphogenesis morphogenesis of a branching epithelium intracellular receptor signaling pathway response to lipid negative regulation of signaling negative regulation of intracellular signal transduction hormone-mediated signaling pathway intracellular signal transduction negative regulation of cell communication negative regulation of intracellular steroid hormone receptor signaling pathway cellular response to endogenous stimulus response to hormone regulation of intracellular signal transduction response to steroid hormone regulation of intracellular steroid hormone receptor signaling pathway regulation of intracellular estrogen receptor signaling pathway negative regulation of cellular process nuclear receptor-mediated steroid hormone signaling pathway cellular response to steroid hormone stimulus negative regulation of intracellular estrogen receptor signaling pathway steroid hormone receptor signaling pathway cellular response to hormone stimulus negative regulation of response to stimulus response to endogenous stimulus negative regulation of signal transduction estrogen receptor signaling pathway cellular response to chemical stimulus response to chemical cellular response to lipid nuclear receptor-mediated signaling pathway skin morphogenesis RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process 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 negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cell surface receptor signaling pathway Notch signaling pathway positive regulation of somatic stem cell population maintenance regulation of somatic stem cell population maintenance regulation of stem cell population maintenance stem cell population maintenance positive regulation of developmental process positive regulation of stem cell population maintenance somatic stem cell population maintenance positive regulation of multicellular organismal process regulation of multicellular organismal process maintenance of cell number positive regulation of DNA-templated transcription 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 transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process epithelial cell development cell development epidermal cell differentiation keratinocyte differentiation positive regulation of keratinocyte proliferation positive regulation of epithelial cell proliferation regulation of keratinocyte proliferation regulation of epithelial cell proliferation polarized epithelial cell differentiation morphogenesis of a polarized epithelium odontogenesis of dentin-containing tooth odontogenesis cranial skeletal system development regulation of epidermal cell differentiation negative regulation of keratinocyte differentiation regulation of cell differentiation regulation of epithelial cell differentiation negative regulation of cell differentiation negative regulation of epidermis development regulation of multicellular organismal development negative regulation of epithelial cell differentiation negative regulation of epidermal cell differentiation regulation of epidermis development negative regulation of multicellular organismal process regulation of keratinocyte differentiation determination of adult lifespan neuron apoptotic process regulation of osteoblast differentiation osteoblast differentiation positive regulation of osteoblast differentiation ossification positive regulation of cell differentiation regulation of cellular senescence negative regulation of cellular senescence regulation of cell cycle phase transition regulation of cell cycle process cell cycle phase transition regulation of cell cycle G1/S phase transition cell cycle G1/S phase transition positive regulation of cell cycle positive regulation of cell cycle G1/S phase transition positive regulation of cell cycle phase transition positive regulation of cell cycle process cell cycle regulation of cell cycle cell cycle process digestive system development tube development cloaca development digestive tract development tube morphogenesis digestive tract morphogenesis cloacal septation signal transduction by p53 class mediator intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator intrinsic apoptotic signaling pathway by p53 class mediator intrinsic apoptotic signaling pathway in response to DNA damage intrinsic apoptotic signaling pathway regulation of Notch signaling pathway positive regulation of Notch signaling pathway pattern specification process regionalization proximal/distal pattern formation establishment of planar polarity establishment of tissue polarity chromatin organization chromatin remodeling	somatodendritic compartment cell projection cellular anatomical structure dendrite dendritic tree neuron projection plasma membrane bounded cell projection intracellular anatomical structure cytoplasm intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin somatodendritic compartment cell projection cellular anatomical structure dendrite dendritic tree neuron projection plasma membrane bounded cell projection intracellular anatomical structure cytoplasm intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR012346	p53/RUNT-type transcription factor, DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR036674	p53-like tetramerisation domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR011615	p53, DNA-binding domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001660	Sterile alpha motif domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR002117	p53 tumour suppressor family	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR008967	p53-like transcription factor, DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR010991	p53, tetramerisation domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR037611	Tumour protein p63, SAM domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	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 A, B, C, D, E, F, G, H	Pharos: Q9H3D4	ADULT syndrome Rapp-Hodgkin syndrome EEC syndrome squamous cell carcinoma cleft palate ankyloblepharon-ectodermal defects-cleft lip/palate syndrome limb-mammary syndrome ectrodactyly, ectodermal dysplasia, and cleft lip-palate syndrome 3 split hand-foot malformation 4 Skin Abnormalities lung adenocarcinoma squamous cell neoplasm bladder exstrophy breast disease split hand-foot malformation ADULT syndrome Rapp-Hodgkin syndrome EEC syndrome squamous cell carcinoma cleft palate ankyloblepharon-ectodermal defects-cleft lip/palate syndrome limb-mammary syndrome ectrodactyly, ectodermal dysplasia, and cleft lip-palate syndrome 3 split hand-foot malformation 4 Skin Abnormalities lung adenocarcinoma squamous cell neoplasm bladder exstrophy breast disease split hand-foot malformation cleft lip sweat gland neoplasm ovarian cancer carcinoma sarcomatoid carcinoma lung carcinoma tubular adenocarcinoma colorectal cancer adenocarcinoma granular cell carcinoma psoriasis intellectual disability childhood acute lymphoblastic leukemia large cell medulloblastoma undifferentiated carcinoma colorectal carcinoma malignant pancreatic neoplasm cribriform carcinoma of breast osteosarcoma esophageal adenocarcinoma pancreatic neoplasm interstitial cystitis lung benign neoplasm malignant colon neoplasm acute lymphoblastic leukemia dermatomyositis myopathy amelogenesis imperfecta non-small cell lung carcinoma Emery-Dreifuss muscular dystrophy breast cancer exocrine pancreatic carcinoma glioblastoma peeling skin syndrome cervical cancer juvenile dermatomyositis cleft lip and alveolus squamous cell lung carcinoma malignant glioma cribriform carcinoma malignant tumor of neck ectrodactyly, ectodermal dysplasia, and cleft lip-palate syndrome 1 amyotrophic lateral sclerosis orofacial cleft 8 atypical teratoid rhabdoid tumor ovarian neoplasm breast carcinoma

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.