1KB4	Transcription Dna	date	Nov 05, 2001
title	Crystal Structure Of Vdr Dna-Binding Domain Bound To A Canonical Direct Repeat With Three Base Pair Spacer (Dr3) Response Element
authors	P.L.Shaffer, D.T.Gewirth
compound		source
Molecule: 5'- D(Cpapcpapgpgptpcpapcpgpapapgpgptpcpa)- 3'; Chain: C Engineered: Yes Other_details: Canonical Direct Repeat With 3 Base Pair Spacer (Dr3) Response Element;		Synthetic: Yes
Molecule: 5'- D(Tpgpapcpcptptpcpgptpgpapcpcptpgptpg)- 3'; Chain: D Engineered: Yes Other_details: Canonical Direct Repeat With 3 Base Pair Spacer (Dr3) Response Element;		Synthetic: Yes
Molecule: Vitamin D3 Receptor Chain: A, B Fragment: Dna-Binding Domain (Residues 16-125) Synonym: Vdr, 1,25-Dihydroxyvitamin D3 Receptor Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Vdr Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet11a-Vdr-N1-Rplks
symmetry	Space Group: P 43 21 2	R_factor 0.214 R_Free 0.272
crystal cell	length a length b length c angle alpha angle beta angle gamma 61.500 61.500 241.970 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.80 Å
ligand	ZN	enzyme
related structures	by homologous chain: 1KB2, 1YNW
Gene Ontology	Chain Function Process Component A, B
Primary reference	Structural basis of VDR-DNA interactions on direct repeat response elements., Shaffer PL, Gewirth DT, EMBO J 2002 May 1;21(9):2242-52. PMID:11980721

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (51 Kb) [Save to disk] Biological Unit Coordinates (1kb4.pdb1.gz) 46 Kb LPC: Ligand-Protein Contacts for 1KB4 CSU: Contacts of Structural Units for 1KB4 Likely Quarternary Molecular Structure file(s) for 1KB4 Structure Factors (126 Kb) Retrieve 1KB4 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1KB4 from S2C, [Save to disk] Re-refined 1kb4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1KB4 in 3D

Proteopedia, because life has more than 2D. On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure. On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Visual 3D analysis of 1KB4

Cartoon representation from PDB Cartoon Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala Dipole moment, from Dipole Server at Weizmann Institute Crystal Contacts, from CryCo at Weizmann Institute 3D motif for 1KB4, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1kb4a_, region A [Jmol] [rasmolscript] [script source]     - Domain d1kb4b_, region B [Jmol] [rasmolscript] [script source] Fold representative 1kb4 from FSSP and Dali (Families of Structurally Similar Proteins) Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH Summaries and structural analyses of PDB data files from PDBSum Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1kb4_A] [1kb4_B] [1kb4] [1kb4_D] [1kb4_C] SWISS-PROT database: [P11473] Domain organization of [VDR_HUMAN] by SWISSPFAM Domain found in 1KB4: [ZnF_C4 ] by SMART Alignments of the sequence of 1KB4 with the sequences similar proteins can be viewed for 1KB4's classification [VDR_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list. A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [VDR_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 1KB4

Community annotation for 1KB4 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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