9BR4 | pdb_00009br4

Crystal structure of p53 Y220C mutant in complex with PC-9859

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
B	SCOP2B Superfamily	p53-like transcription factors	8036866	3000758	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	p53-like transcription factors	8036866	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	Reovirus_L2_GTase	e9br4B1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: Reovirus_L2_GTase	ECOD (v295)
A	Reovirus_L2_GTase	e9br4A1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: Reovirus_L2_GTase	ECOD (v295)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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	Cellular tumor antigen p53	TFIID-class transcription factor complex binding transcription factor binding RNA polymerase binding protein binding binding RNA polymerase II complex binding general transcription initiation factor binding RNA polymerase core enzyme binding enzyme binding RNA polymerase II general transcription initiation factor binding histone deacetylase binding protein-folding chaperone binding chromatin binding promoter-specific chromatin binding TFIID-class transcription factor complex binding transcription factor binding RNA polymerase binding protein binding binding RNA polymerase II complex binding general transcription initiation factor binding RNA polymerase core enzyme binding enzyme binding RNA polymerase II general transcription initiation factor binding histone deacetylase binding protein-folding chaperone binding chromatin binding promoter-specific chromatin binding DNA binding nucleic acid binding ubiquitin protein ligase binding ubiquitin-like protein ligase 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 protein phosphatase binding phosphatase binding protein phosphatase 2A binding protease binding MDM2/MDM4 family protein binding transcription coregulator binding transcription coactivator binding molecular function activator activity molecular function regulator activity sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding transcription regulatory region nucleic acid binding mRNA 3'-UTR binding RNA binding mRNA binding cation binding transition metal ion binding copper ion binding ion binding metal ion binding small molecule binding core promoter sequence-specific DNA binding 14-3-3 protein binding cis-regulatory region sequence-specific DNA binding protein tyrosine kinase binding kinase binding signaling receptor binding receptor tyrosine kinase binding protein kinase binding identical protein binding p53 binding DNA-binding transcription repressor activity, RNA polymerase II-specific DNA-binding transcription repressor activity RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding RNA polymerase II transcription regulatory region sequence-specific DNA binding RNA polymerase II cis-regulatory region sequence-specific DNA binding protein heterodimerization activity protein dimerization activity molecular condensate scaffold activity protein-macromolecule adaptor activity molecular adaptor activity ATP-dependent DNA/DNA annealing activity nucleic acid conformation isomerase activity isomerase activity single-stranded DNA binding catalytic activity, acting on a nucleic acid ATP-dependent activity ATP-dependent activity, acting on DNA DNA/DNA annealing activity catalytic activity, acting on DNA annealing activity catalytic activity macromolecular conformation isomerase activity zinc ion binding disordered domain specific binding protein domain specific binding	regulation of cellular process positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic cellular component organization RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II positive regulation of biosynthetic process chromatin organization regulation of cellular process positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic cellular component organization RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II positive regulation of biosynthetic process chromatin organization chromatin remodeling positive regulation of macromolecule metabolic process cellular component organization or biogenesis positive regulation of cellular process transcription initiation at RNA polymerase II promoter regulation of biosynthetic process regulation of biological process epigenetic regulation of gene expression biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation regulation of gene expression biosynthetic process positive regulation of gene expression transcription initiation-coupled chromatin remodeling regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process cellular response to stimulus response to stimulus signaling signal transduction by p53 class mediator cell death intracellular signal transduction cell communication apoptotic signaling pathway intrinsic apoptotic signaling pathway by p53 class mediator signal transduction apoptotic process intrinsic apoptotic signaling pathway programmed cell death response to chemical response to antibiotic catabolic process autophagy process utilizing autophagic mechanism replicative senescence cell cycle cell cycle process transcription preinitiation complex assembly regulation of primary metabolic process cellular component biogenesis regulation of DNA-templated transcription initiation regulation of RNA metabolic process cellular component assembly regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of DNA-templated transcription initiation positive regulation of RNA metabolic process RNA polymerase II preinitiation complex assembly regulation of DNA-templated transcription regulation of RNA polymerase II transcription preinitiation complex assembly positive regulation of cellular component organization regulation of cellular component organization positive regulation of DNA-templated transcription protein-DNA complex organization positive regulation of protein-containing complex assembly regulation of protein-containing complex assembly protein-containing complex assembly regulation of RNA biosynthetic process positive regulation of RNA polymerase II transcription preinitiation complex assembly protein-containing complex organization positive regulation of cellular component biogenesis positive regulation of transcription initiation by RNA polymerase II protein-DNA complex assembly regulation of cellular component biogenesis positive regulation of RNA biosynthetic process regulation of transcription initiation by RNA polymerase II positive regulation of miRNA transcription positive regulation of miRNA metabolic process miRNA transcription regulation of miRNA metabolic process miRNA metabolic process regulation of miRNA transcription biological process involved in interspecies interaction between organisms response to type II interferon response to cytokine cytokine-mediated signaling pathway cellular response to type II interferon response to biotic stimulus interferon-mediated signaling pathway response to stress innate immune response cellular response to cytokine stimulus response to external biotic stimulus cell surface receptor signaling pathway immune response response to other organism defense response type II interferon-mediated signaling pathway defense response to symbiont response to external stimulus response to peptide immune system process defense response to other organism DNA metabolic process cellular response to stress nucleotide-excision repair DNA damage response DNA repair cellular response to chemical stimulus cellular response to xenobiotic stimulus response to xenobiotic stimulus cellular response to biotic stimulus ER overload response ER-nucleus signaling pathway response to endoplasmic reticulum stress negative regulation of biological process negative regulation of RNA biosynthetic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process negative regulation of small molecule metabolic process carbohydrate catabolic process carbohydrate derivative metabolic process regulation of generation of precursor metabolites and energy negative regulation of nucleotide metabolic process regulation of small molecule metabolic process regulation of nucleotide metabolic process regulation of pentose-phosphate shunt pentose-phosphate shunt pyridine-containing compound metabolic process small molecule metabolic process phosphorus metabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process regulation of carbohydrate catabolic process nucleotide metabolic process regulation of purine nucleotide metabolic process NADP+ metabolic process negative regulation of pentose-phosphate shunt regulation of phosphorus metabolic process negative regulation of purine nucleotide metabolic process glucose 6-phosphate metabolic process purine nucleotide metabolic process nucleobase-containing small molecule metabolic process regulation of NADP metabolic process regulation of carbohydrate metabolic process carbohydrate metabolic process generation of precursor metabolites and energy regulation of catabolic process purine-containing compound metabolic process NADPH regeneration organophosphate metabolic process negative regulation of phosphorus metabolic process negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death negative regulation of apoptotic process negative regulation of ATP-dependent activity regulation of ATP-dependent activity regulation of molecular function regulation of catalytic activity negative regulation of molecular function negative regulation of helicase activity negative regulation of catalytic activity leukocyte apoptotic process positive regulation of thymocyte apoptotic process lymphocyte apoptotic process thymocyte apoptotic process regulation of T cell apoptotic process positive regulation of leukocyte apoptotic process regulation of leukocyte apoptotic process regulation of lymphocyte apoptotic process positive regulation of programmed cell death positive regulation of lymphocyte apoptotic process positive regulation of apoptotic process positive regulation of T cell apoptotic process regulation of thymocyte apoptotic process T cell apoptotic process reactive oxygen species metabolic process positive regulation of reactive oxygen species metabolic process regulation of reactive oxygen species metabolic process small GTPase-mediated signal transduction Ras protein signal transduction intracellular signaling cassette developmental process immune system development multicellular organismal process animal organ development hematopoietic or lymphoid organ development tissue development bone marrow development multicellular organism development skeletal system development anatomical structure development bone development system development regulation of cellular senescence cellular senescence positive regulation of cellular senescence response to ionizing radiation response to radiation response to abiotic stimulus response to gamma radiation localization macromolecule localization intracellular protein localization oligodendrocyte apoptotic process glial cell apoptotic process cell cycle G2/M phase transition regulation of cell cycle phase transition regulation of cell cycle process regulation of cell cycle G2/M phase transition cell cycle phase transition regulation of cell cycle positive regulation of organelle organization apoptotic mitochondrial changes regulation of release of cytochrome c from mitochondria positive regulation of release of cytochrome c from mitochondria mitochondrion organization regulation of organelle organization release of cytochrome c from mitochondria organelle organization regulation of mitochondrion organization protein complex oligomerization protein tetramerization viral process cellular response to nutrient levels response to nutrient levels response to starvation cellular response to glucose starvation cellular response to starvation response to decreased oxygen levels cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels response to hypoxia response to oxygen levels cellular response to ionizing radiation cellular response to radiation cellular response to abiotic stimulus cellular response to environmental stimulus regulation of growth growth negative regulation of cell growth regulation of cell growth cell growth negative regulation of growth DNA damage checkpoint signaling negative regulation of cell cycle regulation of cell cycle G1/S phase transition cell cycle G1/S phase transition mitotic cell cycle negative regulation of mitotic cell cycle regulation of mitotic cell cycle mitotic DNA integrity checkpoint signaling mitotic DNA damage checkpoint signaling negative regulation of cell cycle phase transition negative regulation of G1/S transition of mitotic cell cycle mitotic G1/S transition checkpoint signaling negative regulation of mitotic cell cycle phase transition negative regulation of cell cycle G1/S phase transition DNA integrity checkpoint signaling negative regulation of cell cycle process cell cycle checkpoint signaling regulation of mitotic cell cycle phase transition mitotic cell cycle checkpoint signaling mitotic G1 DNA damage checkpoint signaling mitotic cell cycle process regulation of G1/S transition of mitotic cell cycle signal transduction in response to DNA damage G1/S transition of mitotic cell cycle mitotic cell cycle phase transition regulation of execution phase of apoptosis positive regulation of execution phase of apoptosis execution phase of apoptosis mRNA transcription mRNA metabolic process rhythmic process response to light stimulus entrainment of circadian clock circadian rhythm regulation of circadian rhythm photoperiodism entrainment of circadian clock by photoperiod behavior circadian behavior rhythmic behavior negative regulation of cell population proliferation fibroblast proliferation cell population proliferation regulation of fibroblast proliferation regulation of cell population proliferation negative regulation of fibroblast proliferation positive regulation of cell communication positive regulation of signal transduction regulation of signal transduction regulation of intrinsic apoptotic signaling pathway positive regulation of apoptotic signaling pathway positive regulation of response to stimulus regulation of intracellular signal transduction regulation of signaling positive regulation of intracellular signal transduction regulation of response to stimulus regulation of cell communication positive regulation of intrinsic apoptotic signaling pathway regulation of apoptotic signaling pathway positive regulation of signaling cellular response to tumor necrosis factor tumor necrosis factor-mediated signaling pathway response to tumor necrosis factor programmed necrotic cell death regulation of programmed necrotic cell death positive regulation of programmed necrotic cell death negative regulation of G1 to G0 transition regulation of G1 to G0 transition G1 to G0 transition cellular response to nitrogen compound response to oxygen-containing compound response to nitrogen compound response to actinomycin D cellular response to oxygen-containing compound cellular response to actinomycin D cellular response to antibiotic cellular response to oxidative stress cellular response to chemical stress oxidative stress-induced premature senescence response to oxidative stress stress-induced premature senescence cellular response to gamma radiation negative regulation of telomere maintenance telomere organization negative regulation of telomere maintenance via telomerase regulation of DNA biosynthetic process RNA-templated DNA biosynthetic process telomere maintenance via telomere lengthening negative regulation of chromosome organization negative regulation of cellular component organization regulation of chromosome organization regulation of telomere maintenance via telomere lengthening telomere maintenance DNA biosynthetic process negative regulation of DNA biosynthetic process regulation of DNA metabolic process regulation of telomere maintenance negative regulation of telomere maintenance via telomere lengthening telomere maintenance via telomerase chromosome organization regulation of telomere maintenance via telomerase negative regulation of organelle organization negative regulation of DNA metabolic process determination of adult lifespan stem cell differentiation cellular developmental process cell differentiation hemopoiesis hematopoietic stem cell differentiation cell development hematopoietic progenitor cell differentiation response to UV cellular response to light stimulus cellular response to UV intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress DNA damage response, signal transduction by p53 class mediator intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator intrinsic apoptotic signaling pathway in response to DNA damage	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle membraneless organelle nuclear lumen protein-containing complex mitochondrion mitochondrial matrix transcription regulator complex chromatin chromosome nuclear matrix centrosome microtubule organizing center cytoskeleton microtubule cytoskeleton nucleoplasm endoplasmic reticulum endomembrane system nuclear body PML body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR012346	p53/RUNT-type transcription factor, DNA-binding domain superfamily	Homologous Superfamily
A, B	IPR057064	p53, central conserved site	Conserved Site
A, B	IPR002117	p53 tumour suppressor family	Family
A, B	IPR036674	p53-like tetramerisation domain superfamily	Homologous Superfamily
A, B	IPR011615	p53, DNA-binding domain	Domain
A, B	IPR013872	p53, transactivation domain	Domain
A, B	IPR008967	p53-like transcription factor, DNA-binding domain superfamily	Homologous Superfamily
A, B	IPR010991	p53, tetramerisation domain	Domain
A, B	IPR040926	Cellular tumor antigen p53, transactivation domain 2	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	: P04637	Li-Fraumeni syndrome melanoma cholangiocarcinoma choroid plexus papilloma angiosarcoma B-cell chronic lymphocytic leukemia adrenal cortex carcinoma esophageal cancer adrenocortical carcinoma, hereditary malignant glioma renal cell carcinoma urinary bladder cancer skin basal cell carcinoma squamous cell carcinoma psoriasis Li-Fraumeni syndrome melanoma cholangiocarcinoma choroid plexus papilloma angiosarcoma B-cell chronic lymphocytic leukemia adrenal cortex carcinoma esophageal cancer adrenocortical carcinoma, hereditary malignant glioma renal cell carcinoma urinary bladder cancer skin basal cell carcinoma squamous cell carcinoma psoriasis osteosarcoma head and neck squamous cell carcinoma esophageal squamous cell carcinoma small cell lung carcinoma amyotrophic lateral sclerosis nasopharyngeal carcinoma hypertensive disorder T-cell non-Hodgkin lymphoma adenoma Balkan nephropathy choroid plexus carcinoma hypertrophic cardiomyopathy colorectal cancer kidney Wilms tumor glioblastoma skin neoplasm gallbladder cancer thymoma cancer malignant mesothelioma transitional cell carcinoma non-small cell lung carcinoma cutaneous melanoma esophageal adenocarcinoma primary cutaneous T-cell non-Hodgkin lymphoma breast adenocarcinoma male infertility Neoplasm Metastasis keratosis thyroid gland carcinoma salivary gland adenoid cystic carcinoma astrocytic tumor giant cell glioblastoma carotid artery disease sarcomatoid carcinoma central nervous system cancer ovarian cancer Li-Fraumeni syndrome 1 Sezary syndrome papillary renal cell carcinoma liver cancer small cell carcinoma essential thrombocythemia spindle cell sarcoma microcystic adenoma hepatocellular carcinoma brain ischemia clear cell adenocarcinoma familial pancreatic carcinoma breast cancer collecting duct carcinoma follicular thyroid adenoma thymic carcinoma gastric cancer thyroid adenoma carcinoma tubular adenocarcinoma demyelinating disease sarcomatoid renal cell carcinoma gliosarcoma penile neoplasm adrenal gland cancer polyploidy lung cancer exocrine pancreatic carcinoma mixed glioma myelodysplastic syndrome prostate cancer female infertility breast carcinoma malignant colon neoplasm intrahepatic cholangiocarcinoma vulvar lichen sclerosus adenocarcinoma sarcoma adenoid cystic carcinoma schizophrenia granular cell carcinoma papillary adenoma skin cancer chromophobe renal cell carcinoma lung carcinoma brain glioma mouth disease chronic obstructive pulmonary disease eye disease prostate disease breast disease colorectal adenocarcinoma pulmonary emphysema malignant ependymoma gallbladder neoplasm thymus neoplasm renal carcinoma uterine corpus leiomyoma neuroblastoma acute kidney failure cribriform carcinoma triple-negative breast carcinoma oligodendroglioma acute megakaryoblastic leukemia glioma susceptibility 1 undifferentiated carcinoma granulomatous slack skin disease urinary bladder neoplasm ovarian neoplasm skin disease benign neoplasm of pancreas head and neck carcinoma childhood acute lymphoblastic leukemia penile cancer bile duct cancer medulloblastoma polycystic ovary syndrome lung benign neoplasm bone osteosarcoma lung disease hereditary breast ovarian cancer syndrome primitive neuroectodermal tumor lymphatic system disease subependymal giant cell astrocytoma nasopharyngeal carcinoma, susceptibility to, 1 Burkitt lymphoma neoplasm of esophagus intestinal disease ischemic disease congenital anemia uterine disease neurodegenerative disease cribriform carcinoma of breast SAPHO syndrome atypical teratoid rhabdoid tumor oral cavity neoplasm acute myeloid leukemia ovarian carcinoma Li-Fraumeni syndrome 2 basal cell carcinoma, susceptibility to, 7 malignant pancreatic neoplasm Hantavirus hemorrhagic fever with renal syndrome, Puumala virus type urogenital neoplasm cervical cancer pancreatic neoplasm papilloma epithelioid sarcoma benign urinary system neoplasm head and neck neoplasm uterine cervix carcinoma in situ liver neoplasm esophageal disease bone disease hematopoietic and lymphoid system neoplasm chromosome 17p deletion adult hepatocellular carcinoma brain disease stomach disease hereditary diffuse gastric adenocarcinoma clear cell renal carcinoma nasopharyngeal neoplasm IgA glomerulonephritis colonic neoplasm anemia colorectal carcinoma pustulosis palmaris et plantaris gastric neoplasm thyroid cancer kidney disease rheumatoid arthritis large cell medulloblastoma autoimmune disease glioma urinary bladder disease ovarian disease endometriosis benign colon neoplasm head and neck cancer cervical carcinoma adrenal carcinoma liver disease skin pigmented basal cell carcinoma choroid plexus cancer pilocytic astrocytoma bone marrow disease metabolic syndrome X hepatoblastoma

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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.