General information
PDB ID 4IBU
Title HUMAN P53 CORE DOMAIN WITH HOT SPOT MUTATION R273C AND SECOND-SITE SUPPRESSOR MUTATION T284R IN SEQUENCE-SPECIFIC COMPLEX WITH DNA
PDB header DNA BINDING PROTEIN/DNA
Date 2012-12-09
Experimental method X-RAY DIFFRACTION
Resolution (A) 1.7
Kind dna
Organism HOMO SAPIENS
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PDB PDBe MMDB Jena OCA
CATH PDBsum HSSP PDBePISA UniProt
ProteopediA BIPA
 PDIdb 
Composition of PDB entry and biounits
File: Protein chains: DNA chains: RNA chains: No. of models: Action:
PDB entry:
pdb4ibu.pdb ABCD EFGH 0
Biounits:
4ibu.pdb1.pdb ABCD EFGH 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
P53 Domain P04637_99-289 1.3e-60 1 CL0073 A 99 289 EFG  H-Bb H-Mj S-Bb S-Mj L-Bb L-Mj L-Mn 
P53 Domain P04637_99-289 1.3e-60 1 CL0073 B 99 289 EF  H-Bb H-Mj S-Bb L-Bb L-Mj L-Mn 
P53 Domain P04637_99-289 1.2e-60 1 CL0073 C 99 289 FGH  H-Bb H-Mj S-Bb L-Bb L-Mj L-Mn 
P53 Domain P04637_99-289 1.2e-60 1 CL0073 D 99 289 GH  H-Bb H-Mj S-Bb L-Bb L-Mj 
SCOP domains
No SCOP domains
GO terms
Protein chains: GO type: GO description:
A/B/C/D=94-293 C centrosome
A/B/C/D=94-293 C cytoplasm
A/B/C/D=94-293 C cytosol
A/B/C/D=94-293 C endoplasmic reticulum
A/B/C/D=94-293 C mitochondrial matrix
A/B/C/D=94-293 C mitochondrion
A/B/C/D=94-293 C nuclear chromatin
A/B/C/D=94-293 C nuclear matrix
A/B/C/D=94-293 C nuclear membrane
A/B/C/D=94-293 C nucleolus
A/B/C/D=94-293 C nucleoplasm
A/B/C/D=94-293 C nucleus
A/B/C/D=94-293 C PML body
A/B/C/D=94-293 C protein-containing complex
A/B/C/D=94-293 C replication fork
A/B/C/D=94-293 C site of double-strand break
A/B/C/D=94-293 C transcription regulator complex
A/B/C/D=94-293 F ATP binding
A/B/C/D=94-293 F chaperone binding
A/B/C/D=94-293 F chromatin binding
A/B/C/D=94-293 F copper ion binding
A/B/C/D=94-293 F core promoter sequence-specific DNA binding
A/B/C/D=94-293 F disordered domain specific binding
A/B/C/D=94-293 F DNA binding
A/B/C/D=94-293 F DNA-binding transcription activator activity, RNA polymerase II-specific
A/B/C/D=94-293 F DNA-binding transcription factor activity
A/B/C/D=94-293 F DNA-binding transcription factor activity, RNA polymerase II-specific
A/B/C/D=94-293 F enzyme binding
A/B/C/D=94-293 F histone acetyltransferase binding
A/B/C/D=94-293 F histone deacetylase binding
A/B/C/D=94-293 F histone deacetylase regulator activity
A/B/C/D=94-293 F identical protein binding
A/B/C/D=94-293 F MDM2/MDM4 family protein binding
A/B/C/D=94-293 F mRNA 3'-UTR binding
A/B/C/D=94-293 F p53 binding
A/B/C/D=94-293 F promoter-specific chromatin binding
A/B/C/D=94-293 F protease binding
A/B/C/D=94-293 F protein heterodimerization activity
A/B/C/D=94-293 F protein kinase binding
A/B/C/D=94-293 F protein N-terminus binding
A/B/C/D=94-293 F protein phosphatase 2A binding
A/B/C/D=94-293 F protein phosphatase binding
A/B/C/D=94-293 F protein self-association
A/B/C/D=94-293 F receptor tyrosine kinase binding
A/B/C/D=94-293 F RNA polymerase II cis-regulatory region sequence-specific DNA binding
A/B/C/D=94-293 F RNA polymerase II transcription factor binding
A/B/C/D=94-293 F TFIID-class transcription factor complex binding
A/B/C/D=94-293 F transcription factor binding
A/B/C/D=94-293 F transcription regulatory region sequence-specific DNA binding
A/B/C/D=94-293 F ubiquitin protein ligase binding
A/B/C/D=94-293 F zinc ion binding
A/B/C/D=94-293 P autophagy
A/B/C/D=94-293 P B cell lineage commitment
A/B/C/D=94-293 P bone marrow development
A/B/C/D=94-293 P cardiac septum morphogenesis
A/B/C/D=94-293 P cell aging
A/B/C/D=94-293 P cell cycle arrest
A/B/C/D=94-293 P cellular protein localization
A/B/C/D=94-293 P cellular response to actinomycin D
A/B/C/D=94-293 P cellular response to DNA damage stimulus
A/B/C/D=94-293 P cellular response to drug
A/B/C/D=94-293 P cellular response to gamma radiation
A/B/C/D=94-293 P cellular response to glucose starvation
A/B/C/D=94-293 P cellular response to hypoxia
A/B/C/D=94-293 P cellular response to ionizing radiation
A/B/C/D=94-293 P cellular response to UV
A/B/C/D=94-293 P cellular response to UV-C
A/B/C/D=94-293 P cerebellum development
A/B/C/D=94-293 P chromatin assembly
A/B/C/D=94-293 P circadian behavior
A/B/C/D=94-293 P cytokine-mediated signaling pathway
A/B/C/D=94-293 P determination of adult lifespan
A/B/C/D=94-293 P DNA damage response, signal transduction by p53 class mediator
A/B/C/D=94-293 P DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest
A/B/C/D=94-293 P DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator
A/B/C/D=94-293 P DNA strand renaturation
A/B/C/D=94-293 P double-strand break repair
A/B/C/D=94-293 P embryonic organ development
A/B/C/D=94-293 P entrainment of circadian clock by photoperiod
A/B/C/D=94-293 P ER overload response
A/B/C/D=94-293 P gastrulation
A/B/C/D=94-293 P hematopoietic progenitor cell differentiation
A/B/C/D=94-293 P hematopoietic stem cell differentiation
A/B/C/D=94-293 P in utero embryonic development
A/B/C/D=94-293 P interferon-gamma-mediated signaling pathway
A/B/C/D=94-293 P intrinsic apoptotic signaling pathway
A/B/C/D=94-293 P intrinsic apoptotic signaling pathway by p53 class mediator
A/B/C/D=94-293 P intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
A/B/C/D=94-293 P intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress
A/B/C/D=94-293 P intrinsic apoptotic signaling pathway in response to hypoxia
A/B/C/D=94-293 P mitochondrial DNA repair
A/B/C/D=94-293 P mitotic cell cycle arrest
A/B/C/D=94-293 P mitotic G1 DNA damage checkpoint
A/B/C/D=94-293 P mRNA transcription
A/B/C/D=94-293 P multicellular organism growth
A/B/C/D=94-293 P necroptotic process
A/B/C/D=94-293 P negative regulation of apoptotic process
A/B/C/D=94-293 P negative regulation of cell growth
A/B/C/D=94-293 P negative regulation of cell population proliferation
A/B/C/D=94-293 P negative regulation of DNA replication
A/B/C/D=94-293 P negative regulation of fibroblast proliferation
A/B/C/D=94-293 P negative regulation of glucose catabolic process to lactate via pyruvate
A/B/C/D=94-293 P negative regulation of helicase activity
A/B/C/D=94-293 P negative regulation of mitophagy
A/B/C/D=94-293 P negative regulation of neuroblast proliferation
A/B/C/D=94-293 P negative regulation of pentose-phosphate shunt
A/B/C/D=94-293 P negative regulation of production of miRNAs involved in gene silencing by miRNA
A/B/C/D=94-293 P negative regulation of proteolysis
A/B/C/D=94-293 P negative regulation of reactive oxygen species metabolic process
A/B/C/D=94-293 P negative regulation of telomerase activity
A/B/C/D=94-293 P negative regulation of transcription by RNA polymerase II
A/B/C/D=94-293 P negative regulation of transcription, DNA-templated
A/B/C/D=94-293 P negative regulation of transforming growth factor beta receptor signaling pathway
A/B/C/D=94-293 P neuron apoptotic process
A/B/C/D=94-293 P nucleotide-excision repair
A/B/C/D=94-293 P oligodendrocyte apoptotic process
A/B/C/D=94-293 P oxidative stress-induced premature senescence
A/B/C/D=94-293 P positive regulation of apoptotic process
A/B/C/D=94-293 P positive regulation of cardiac muscle cell apoptotic process
A/B/C/D=94-293 P positive regulation of cell aging
A/B/C/D=94-293 P positive regulation of cell cycle arrest
A/B/C/D=94-293 P positive regulation of execution phase of apoptosis
A/B/C/D=94-293 P positive regulation of gene expression
A/B/C/D=94-293 P positive regulation of histone deacetylation
A/B/C/D=94-293 P positive regulation of intrinsic apoptotic signaling pathway
A/B/C/D=94-293 P positive regulation of mitochondrial membrane permeability
A/B/C/D=94-293 P positive regulation of neuron apoptotic process
A/B/C/D=94-293 P positive regulation of peptidyl-tyrosine phosphorylation
A/B/C/D=94-293 P positive regulation of pri-miRNA transcription by RNA polymerase II
A/B/C/D=94-293 P positive regulation of production of miRNAs involved in gene silencing by miRNA
A/B/C/D=94-293 P positive regulation of programmed necrotic cell death
A/B/C/D=94-293 P positive regulation of protein export from nucleus
A/B/C/D=94-293 P positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway
A/B/C/D=94-293 P positive regulation of reactive oxygen species metabolic process
A/B/C/D=94-293 P positive regulation of release of cytochrome c from mitochondria
A/B/C/D=94-293 P positive regulation of RNA polymerase II transcription preinitiation complex assembly
A/B/C/D=94-293 P positive regulation of thymocyte apoptotic process
A/B/C/D=94-293 P positive regulation of transcription by RNA polymerase II
A/B/C/D=94-293 P positive regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress
A/B/C/D=94-293 P positive regulation of transcription from RNA polymerase II promoter in response to hypoxia
A/B/C/D=94-293 P positive regulation of transcription from RNA polymerase II promoter in response to stress
A/B/C/D=94-293 P positive regulation of transcription, DNA-templated
A/B/C/D=94-293 P protein deubiquitination
A/B/C/D=94-293 P protein import into nucleus
A/B/C/D=94-293 P protein localization
A/B/C/D=94-293 P protein stabilization
A/B/C/D=94-293 P protein tetramerization
A/B/C/D=94-293 P protein-containing complex assembly
A/B/C/D=94-293 P Ras protein signal transduction
A/B/C/D=94-293 P regulation of apoptotic process
A/B/C/D=94-293 P regulation of cell cycle G2/M phase transition
A/B/C/D=94-293 P regulation of cellular senescence
A/B/C/D=94-293 P regulation of DNA damage response, signal transduction by p53 class mediator
A/B/C/D=94-293 P regulation of fibroblast apoptotic process
A/B/C/D=94-293 P regulation of intrinsic apoptotic signaling pathway by p53 class mediator
A/B/C/D=94-293 P regulation of mitochondrial membrane permeability involved in apoptotic process
A/B/C/D=94-293 P regulation of signal transduction by p53 class mediator
A/B/C/D=94-293 P regulation of tissue remodeling
A/B/C/D=94-293 P regulation of transcription from RNA polymerase II promoter in response to DNA damage
A/B/C/D=94-293 P regulation of transcription, DNA-templated
A/B/C/D=94-293 P release of cytochrome c from mitochondria
A/B/C/D=94-293 P replicative senescence
A/B/C/D=94-293 P response to antibiotic
A/B/C/D=94-293 P response to gamma radiation
A/B/C/D=94-293 P response to ischemia
A/B/C/D=94-293 P response to salt stress
A/B/C/D=94-293 P response to X-ray
A/B/C/D=94-293 P rRNA transcription
A/B/C/D=94-293 P signal transduction by p53 class mediator
A/B/C/D=94-293 P somitogenesis
A/B/C/D=94-293 P T cell differentiation in thymus
A/B/C/D=94-293 P T cell lineage commitment
A/B/C/D=94-293 P T cell proliferation involved in immune response
A/B/C/D=94-293 P transforming growth factor beta receptor signaling pathway
A/B/C/D=94-293 P tumor necrosis factor-mediated signaling pathway
A/B/C/D=94-293 P viral process
Sequences
Download file with secondary structure created by Stride  
4ibu.pdb1.pdb:   [ download sequences in FASTA format ]
E (dna): 
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F (dna): 
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G (dna): 
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H (dna): 
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A (protein): 
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B (protein): 
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C (protein): 
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D (protein): 
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