General information
PDB ID 1VKX
Title CRYSTAL STRUCTURE OF THE NFKB P50/P65 HETERODIMER COMPLEXED TO THE IMMUNOGLOBULIN KB DNA
PDB header TRANSCRIPTION/DNA
Date 1997-09-17
Experimental method X-RAY DIFFRACTION
Resolution (A) 2.9
Kind dna
Organism MUS MUSCULUS
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PDB PDBe MMDB Jena OCA
CATH PDBsum HSSP PDBePISA UniProt
ProteopediA BIPA
Composition of PDB entry and biounits
File: Protein chains: DNA chains: RNA chains: No. of models: Action:
PDB entry:
pdb1vkx.pdb AB CD 0
Biounits:
1vkx.pdb1.pdb AB CD 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
RHD_DNA_bind Domain Q04207_21-186 7.9e-70 1 CL0073 A 21 186 CD  H-Bb S-Bb S-Mj L-Bb L-Mj 
RHD_dimer Domain Q04207_195-291 9.3e-37 1 CL0159 A 195 291 C  L-Bb 
RHD_DNA_bind Domain P25799_42-240 8.3e-74 1 CL0073 B 342 540 CD  H-Bb S-Bb S-Mj L-Bb L-Mj 
RHD_dimer Domain P25799_249-350 2.9e-40 1 CL0159 B 549 650 D  L-Bb 
SCOP domains
Classification: Protein: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
Class: All beta proteins
  Fold: Immunoglobulin-like beta-sandwich
    Superfamily: E set domains
      Family: NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain
p50 subunit of NF-kappa B transcription factor B 547 650 D  L-Bb 
Class: All beta proteins
  Fold: Immunoglobulin-like beta-sandwich
    Superfamily: E set domains
      Family: NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain
p65 subunit of NF-kappa B (NFKB), dimerization domain A 192 291 C  L-Bb 
Class: All beta proteins
  Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f
    Superfamily: p53-like transcription factors
      Family: Rel/Dorsal transcription factors, DNA-binding domain
p50 subunit of NF-kappa B (NFKB), N-terminal domain B 339 546 CD  H-Bb S-Bb S-Mj L-Bb L-Mj 
Class: All beta proteins
  Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f
    Superfamily: p53-like transcription factors
      Family: Rel/Dorsal transcription factors, DNA-binding domain
p65 subunit of NF-kappa B (NFKB), N-terminal domain A 19 191 CD  H-Bb S-Bb S-Mj L-Bb L-Mj 
GO terms
Protein chains: GO type: GO description:
A=20-291 C cytoplasm
A=20-291 C cytosol
A=20-291 C glutamatergic synapse
A=20-291 C host cell nucleus
A=20-291 C NF-kappaB complex
A=20-291 C NF-kappaB p50/p65 complex
A=20-291 C nuclear chromatin
A=20-291 C nucleoplasm
A=20-291 C nucleus
A=20-291 C protein-containing complex
A=20-291 C synapse
A=20-291 C transcription regulator complex
A=20-291 F actinin binding
A=20-291 F activating transcription factor binding
A=20-291 F ankyrin repeat binding
A=20-291 F chromatin binding
A=20-291 F chromatin DNA binding
A=20-291 F DNA binding
A=20-291 F DNA-binding transcription activator activity, RNA polymerase II-specific
A=20-291 F DNA-binding transcription factor activity
A=20-291 F DNA-binding transcription factor activity, RNA polymerase II-specific
A=20-291 F DNA-binding transcription repressor activity, RNA polymerase II-specific
A=20-291 F enzyme binding
A=20-291 F histone deacetylase binding
A=20-291 F identical protein binding
A=20-291 F NF-kappaB binding
A=20-291 F peptide binding
A=20-291 F phosphate ion binding
A=20-291 F protein homodimerization activity
A=20-291 F protein kinase binding
A=20-291 F protein N-terminus binding
A=20-291 F protein-containing complex binding
A=20-291 F repressing transcription factor binding
A=20-291 F RNA polymerase II cis-regulatory region sequence-specific DNA binding
A=20-291 F RNA polymerase II core promoter sequence-specific DNA binding
A=20-291 F RNA polymerase II transcription coactivator binding
A=20-291 F RNA polymerase II transcription regulatory region sequence-specific DNA binding
A=20-291 F sequence-specific DNA binding
A=20-291 F transcription factor binding
A=20-291 F transcription regulatory region sequence-specific DNA binding
A=20-291 F ubiquitin protein ligase binding
A=20-291 P acetaldehyde metabolic process
A=20-291 P aging
A=20-291 P animal organ morphogenesis
A=20-291 P cellular response to angiotensin
A=20-291 P cellular response to hepatocyte growth factor stimulus
A=20-291 P cellular response to hydrogen peroxide
A=20-291 P cellular response to interleukin-1
A=20-291 P cellular response to interleukin-6
A=20-291 P cellular response to lipopolysaccharide
A=20-291 P cellular response to lipoteichoic acid
A=20-291 P cellular response to nicotine
A=20-291 P cellular response to peptidoglycan
A=20-291 P cellular response to tumor necrosis factor
A=20-291 P cellular response to vascular endothelial growth factor stimulus
A=20-291 P chromatin organization
A=20-291 P cytokine-mediated signaling pathway
A=20-291 P defense response
A=20-291 P hair follicle development
A=20-291 P I-kappaB kinase/NF-kappaB signaling
A=20-291 P inflammatory response
A=20-291 P innate immune response
A=20-291 P interleukin-1-mediated signaling pathway
A=20-291 P liver development
A=20-291 P negative regulation of apoptotic process
A=20-291 P negative regulation of extrinsic apoptotic signaling pathway
A=20-291 P negative regulation of insulin receptor signaling pathway
A=20-291 P negative regulation of NIK/NF-kappaB signaling
A=20-291 P negative regulation of pri-miRNA transcription by RNA polymerase II
A=20-291 P negative regulation of protein catabolic process
A=20-291 P negative regulation of protein sumoylation
A=20-291 P negative regulation of transcription by RNA polymerase II
A=20-291 P negative regulation of transcription, DNA-templated
A=20-291 P NIK/NF-kappaB signaling
A=20-291 P nucleotide-binding oligomerization domain containing 2 signaling pathway
A=20-291 P positive regulation of amyloid-beta formation
A=20-291 P positive regulation of cell population proliferation
A=20-291 P positive regulation of chondrocyte differentiation
A=20-291 P positive regulation of I-kappaB kinase/NF-kappaB signaling
A=20-291 P positive regulation of interleukin-12 production
A=20-291 P positive regulation of interleukin-8 production
A=20-291 P positive regulation of leukocyte adhesion to vascular endothelial cell
A=20-291 P positive regulation of miRNA metabolic process
A=20-291 P positive regulation of NF-kappaB transcription factor activity
A=20-291 P positive regulation of NIK/NF-kappaB signaling
A=20-291 P positive regulation of pri-miRNA transcription by RNA polymerase II
A=20-291 P positive regulation of Schwann cell differentiation
A=20-291 P positive regulation of T cell receptor signaling pathway
A=20-291 P positive regulation of transcription by RNA polymerase II
A=20-291 P positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus
A=20-291 P positive regulation of transcription, DNA-templated
A=20-291 P postsynapse to nucleus signaling pathway
A=20-291 P regulation of DNA-templated transcription in response to stress
A=20-291 P regulation of inflammatory response
A=20-291 P regulation of NIK/NF-kappaB signaling
A=20-291 P regulation of transcription, DNA-templated
A=20-291 P response to amino acid
A=20-291 P response to bacterium
A=20-291 P response to cAMP
A=20-291 P response to cobalamin
A=20-291 P response to cytokine
A=20-291 P response to drug
A=20-291 P response to insulin
A=20-291 P response to interleukin-1
A=20-291 P response to morphine
A=20-291 P response to muramyl dipeptide
A=20-291 P response to muscle stretch
A=20-291 P response to organic substance
A=20-291 P response to progesterone
A=20-291 P response to UV-B
A=20-291 P transcription, DNA-templated
A=20-291 P tumor necrosis factor-mediated signaling pathway
B=39-350 C cytoplasm
B=39-350 C cytosol
B=39-350 C host cell nucleus
B=39-350 C mitochondrion
B=39-350 C neuron projection
B=39-350 C nucleoplasm
B=39-350 C nucleus
B=39-350 C protein-containing complex
B=39-350 F actinin binding
B=39-350 F chromatin binding
B=39-350 F DNA binding
B=39-350 F DNA-binding transcription activator activity, RNA polymerase II-specific
B=39-350 F DNA-binding transcription factor activity
B=39-350 F DNA-binding transcription repressor activity, RNA polymerase II-specific
B=39-350 F double-stranded DNA binding
B=39-350 F enzyme binding
B=39-350 F heat shock protein binding
B=39-350 F identical protein binding
B=39-350 F protein-containing complex binding
B=39-350 F RNA polymerase II cis-regulatory region sequence-specific DNA binding
B=39-350 F RNA polymerase II transcription coactivator binding
B=39-350 F RNA polymerase II transcription regulatory region sequence-specific DNA binding
B=39-350 F sequence-specific DNA binding
B=39-350 F transcription regulatory region sequence-specific DNA binding
B=39-350 P apoptotic process
B=39-350 P cellular response to angiotensin
B=39-350 P cellular response to brain-derived neurotrophic factor stimulus
B=39-350 P cellular response to carbohydrate stimulus
B=39-350 P cellular response to cytokine stimulus
B=39-350 P cellular response to diterpene
B=39-350 P cellular response to dsRNA
B=39-350 P cellular response to glucoside
B=39-350 P cellular response to interleukin-1
B=39-350 P cellular response to interleukin-6
B=39-350 P cellular response to lipopolysaccharide
B=39-350 P cellular response to mechanical stimulus
B=39-350 P cellular response to nicotine
B=39-350 P cellular response to organic cyclic compound
B=39-350 P cellular response to peptide
B=39-350 P cellular response to tumor necrosis factor
B=39-350 P lymph node development
B=39-350 P negative regulation of apoptotic process
B=39-350 P negative regulation of calcidiol 1-monooxygenase activity
B=39-350 P negative regulation of cytokine production
B=39-350 P negative regulation of gene expression
B=39-350 P negative regulation of inflammatory response
B=39-350 P negative regulation of interleukin-12 production
B=39-350 P negative regulation of transcription by RNA polymerase II
B=39-350 P negative regulation of transcription, DNA-templated
B=39-350 P positive regulation of canonical Wnt signaling pathway
B=39-350 P positive regulation of gene expression
B=39-350 P positive regulation of gene silencing by miRNA
B=39-350 P positive regulation of hyaluronan biosynthetic process
B=39-350 P positive regulation of miRNA metabolic process
B=39-350 P positive regulation of pri-miRNA transcription by RNA polymerase II
B=39-350 P positive regulation of transcription by RNA polymerase II
B=39-350 P positive regulation of transcription, DNA-templated
B=39-350 P response to muscle stretch
B=39-350 P response to organic cyclic compound
B=39-350 P response to oxidative stress
B=39-350 P signal transduction
Sequences
Download file with secondary structure created by Stride  
1vkx.pdb1.pdb:   [ download sequences in FASTA format ]
C (dna): 
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D (dna): 
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A (protein): 
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B (protein): 
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