2HBH | pdb_00002hbh

Crystal structure of Vitamin D nuclear receptor ligand binding domain bound to a locked side-chain analog of calcitriol and SRC-1 peptide

PDB DOI: https://doi.org/10.2210/pdb2HBH/pdb

Classification: GENE REGULATION
Organism(s): Danio rerio, Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2006-06-14 Released: 2007-05-01
Deposition Author(s): Rochel, N., Hourai, S., Moras, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.261 (Depositor), 0.254 (DCC)
R-Value Work:
0.203 (Depositor), 0.190 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal structure of the vitamin D nuclear receptor ligand binding domain in complex with a locked side chain analog of calcitriol

Rochel, N., Hourai, S., Perez-Garcia, X., Rumbo, A., Mourino, A., Moras, D.

(2007) Arch Biochem Biophys 460: 172-176

PubMed: 17346665 Search on PubMed
DOI: https://doi.org/10.1016/j.abb.2007.01.031
Primary Citation Related Structures:
2HBH

PubMed Abstract:
The crystal structures of vitamin D nuclear receptor (VDR) have revealed that all compounds are anchored by the same residues to the ligand binding pocket (LBP). Based on this observation, a synthetic analog with a locked side chain (21-nor-calcitriol-20(22),23-diyne) has been synthesized in order to gain in entropy energy with a predefined active side chain conformation. The crystal structure of VDR LBD bound to this locked side chain analogue while confirming the docking provides a structural basis for the activity of this compound.

Organizational Affiliation

Institut de Génétique et de Biologie Moléculaire et Cellulaire, Département de Biologie et de Génomique Structurales, Illkirch F-67400, France.

Macromolecule Content

Total Structure Weight: 36.23 kDa
Atom Count: 2,109
Modeled Residue Count: 249
Deposited Residue Count: 317
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vitamin D receptor	A	302	Danio rerio	Mutation(s): 0
UniProt
Find proteins for Q9PTN2 (Danio rerio) Explore Q9PTN2 Go to UniProtKB: Q9PTN2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9PTN2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SRC-1 from Nuclear receptor coactivator 1	B	15	Homo sapiens	Mutation(s): 0 EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q15788 (Homo sapiens) Explore Q15788 Go to UniProtKB: Q15788
PHAROS: Q15788 GTEx: ENSG00000084676
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15788
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XE4 Query on XE4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	1,3-CYCLOHEXANEDIOL, 4-METHYLENE-5-[(2E)-[(1S,3AS,7AS)-OCTAHYDRO-1-(5-HYDROXY-5-METHYL-1,3-HEXADIYNYL)-7A-METHYL-4H-INDEN-4-YLIDENE]ETHYLIDENE]-, (1R,3S,5Z) C₂₆ H₃₄ O₃ CEEUUHVULXTFGS-BQXVGYHGSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.261 (Depositor), 0.254 (DCC)
R-Value Work: 0.203 (Depositor), 0.190 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.682	α = 90
b = 65.682	β = 90
c = 265.096	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
HKL-2000	data scaling
CNS	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-05-01

Deposition Author(s):

Rochel, N.

Hourai, S.

Moras, D.

Revision History (Full details and data files)

Version 1.0: 2007-05-01
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2021-03-03
Changes: Database references, Derived calculations, Source and taxonomy
Version 1.4: 2023-10-25
Changes: Data collection, Database references, Refinement description