1kb2 Summary

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Crystal Structure of VDR DNA-binding Domain Bound to Mouse Osteopontin (SPP) Response Element

The structure was published by Shaffer, P.L. and Gewirth, D.T., in 2002 in a paper entitled "Structural basis of VDR-DNA interactions on direct repeat response elements." (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 2.7 Å and deposited in 2001.

The experimental data on which the structure is based was also deposited.

This PDB entry contains a complex of 3 biomacromolecules, namely 5'-D(*CP*AP*CP*GP*GP*TP*TP*CP*AP*CP*GP*AP*GP*GP*TP*TP*CP*A)-3', 5'-D(*TP*GP*AP*AP*CP*CP*TP*CP*GP*TP*GP*AP*AP*CP*CP*GP*TP*G)-3', and Vitamin D3 Receptor.

It also contains one or more heterogenic compounds (e.g., ligands, co-factors, ions, modified amino acids, etc.); see here for a complete list.

The molecule most likely forms heterotetramers.

The following tables show cross-reference information to other databases (to obtain a list of all PDB entries sharing the same property or classification, click on the magnifying glass icon):


Chain Name UniProt Name of source organism % of UniProt sequence present in the sample Residues in the sample molecules % of residues observed
A Vitamin D3 Receptor P11473 (16-125) (VDR_HUMAN)search Homo sapienssearch < 90% 110 80%
B Vitamin D3 Receptor P11473 (16-125) (VDR_HUMAN)search Homo sapienssearch < 90% 110 80%


This entry contains 1 unique UniProt protein:

UniProt accession Name Organism PDB
P11473 (16 - 125) Vitamin D3 Receptor Homo sapiens

Chain Structural classification (SCOP) Structural classification (CATH) Sequence family (Pfam)
A, B Nuclear receptorsearch Erythroid Transcription Factor GATA-1, subunit Asearch Zinc finger, C4 type (two domains)search

Chain ID Cellular component (GO) Molecular function (GO) Biological process (GO)
A, B (P11473) nucleussearch zinc ion bindingsearch sequence-specific DNA binding transcription factor activitysearch steroid hormone receptor activitysearch sequence-specific DNA bindingsearch regulation of transcription, DNA-templatedsearch

Chain InterPro annotation
A, B Zinc finger, nuclear hormone receptor-typesearch Nuclear hormone receptor, ligand-bindingsearch Zinc finger, NHR/GATA-typesearch