General information
PDB ID 1KB4
Title CRYSTAL STRUCTURE OF VDR DNA-BINDING DOMAIN BOUND TO A CANONICAL DIRECT REPEAT WITH THREE BASE PAIR SPACER (DR3) RESPONSE ELEMENT
PDB header TRANSCRIPTION/DNA
Date 2001-11-05
Experimental method X-RAY DIFFRACTION
Resolution (A) 2.8
Kind dna
Organism HOMO SAPIENS
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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:
pdb1kb4.pdb AB CD 0
Biounits:
1kb4.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:
zf-C4 Domain P11473_22-91 7.7e-30 1 CL0167 A 22 91 CD  H-Bb H-Mj S-Bb L-Bb 
zf-C4 Domain P11473_22-91 9.5e-30 1 CL0167 B 222 291 CD  H-Bb H-Mj S-Bb L-Bb 
SCOP domains
Classification: Protein: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
Class: Small proteins
  Fold: Glucocorticoid receptor-like (DNA-binding domain)
    Superfamily: Glucocorticoid receptor-like (DNA-binding domain)
      Family: Nuclear receptor
Vitamin D3 receptor, VDR, DNA-binding domain A N/A N/A CD  H-Bb H-Mj S-Bb L-Bb 
Class: Small proteins
  Fold: Glucocorticoid receptor-like (DNA-binding domain)
    Superfamily: Glucocorticoid receptor-like (DNA-binding domain)
      Family: Nuclear receptor
Vitamin D3 receptor, VDR, DNA-binding domain B N/A N/A CD  H-Bb H-Mj S-Bb L-Bb 
GO terms
Protein chains: GO type: GO description:
A/B=16-125 C cytosol
A/B=16-125 C nuclear chromatin
A/B=16-125 C nucleoplasm
A/B=16-125 C nucleus
A/B=16-125 C receptor complex
A/B=16-125 C RNA polymerase II transcription regulator complex
A/B=16-125 F calcitriol binding
A/B=16-125 F DNA binding
A/B=16-125 F DNA-binding transcription factor activity, RNA polymerase II-specific
A/B=16-125 F lithocholic acid binding
A/B=16-125 F lithocholic acid receptor activity
A/B=16-125 F nuclear receptor activity
A/B=16-125 F retinoid X receptor binding
A/B=16-125 F RNA polymerase II transcription regulatory region sequence-specific DNA binding
A/B=16-125 F signaling receptor activity
A/B=16-125 F transcription factor binding
A/B=16-125 F zinc ion binding
A/B=16-125 P bile acid signaling pathway
A/B=16-125 P calcium ion transport
A/B=16-125 P cell differentiation
A/B=16-125 P cell morphogenesis
A/B=16-125 P cellular calcium ion homeostasis
A/B=16-125 P cholesterol homeostasis
A/B=16-125 P decidualization
A/B=16-125 P intestinal absorption
A/B=16-125 P lactation
A/B=16-125 P lipid homeostasis
A/B=16-125 P lipid metabolic process
A/B=16-125 P mammary gland branching involved in pregnancy
A/B=16-125 P multicellular organism development
A/B=16-125 P negative regulation of cell population proliferation
A/B=16-125 P negative regulation of gene expression
A/B=16-125 P negative regulation of keratinocyte proliferation
A/B=16-125 P negative regulation of transcription by RNA polymerase II
A/B=16-125 P negative regulation of transcription, DNA-templated
A/B=16-125 P positive regulation of apoptotic process involved in mammary gland involution
A/B=16-125 P positive regulation of gene expression
A/B=16-125 P positive regulation of keratinocyte differentiation
A/B=16-125 P positive regulation of transcription by RNA polymerase II
A/B=16-125 P positive regulation of vitamin D 24-hydroxylase activity
A/B=16-125 P regulation of calcidiol 1-monooxygenase activity
A/B=16-125 P skeletal system development
A/B=16-125 P transcription initiation from RNA polymerase II promoter
A/B=16-125 P vitamin D metabolic process
A/B=16-125 P vitamin D receptor signaling pathway
Sequences
Download file with secondary structure created by Stride  
1kb4.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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