5GT4 | pdb_00005gt4

Crystal structure of the human vitamin D receptor ligand binding domain complexed with (1R,2S,3R,5Z,7E,14beta,17alpha)-2-cyanopropoxy-9,10-secocholesta-5,7,10-triene-1,3,25-triol

PDB DOI: https://doi.org/10.2210/pdb5GT4/pdb
Entry: 5GT4 supersedes: 4PA2

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-08-18 Released: 2016-11-09
Deposition Author(s): Takimoto-Kamimura, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free:
0.217 (Depositor), 0.225 (DCC)
R-Value Work:
0.190 (Depositor), 0.199 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of the human vitamin D receptor ligand binding domain complexed with (1R,2S,3R,5Z,7E,14beta,17alpha)-2-cyanopropoxy-9,10-secocholesta-5,7,10-triene-1,3,25-triol

Takimoto-Kamimura, M.

To be published.

Macromolecule Content

Total Structure Weight: 29.45 kDa
Atom Count: 2,171
Modeled Residue Count: 255
Deposited Residue Count: 255
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vitamin D3 receptor	A	255	Homo sapiens	Mutation(s): 0 Gene Names: VDR, NR1I1
UniProt & NIH Common Fund Data Resources
Find proteins for P11473 (Homo sapiens) Explore P11473 Go to UniProtKB: P11473
PHAROS: P11473 GTEx: ENSG00000111424
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11473
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2KB Query on 2KB Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	4-{[(1R,2S,3R,5Z,7E,14beta,17alpha)-1,3,25-trihydroxy-9,10-secocholesta-5,7,10-trien-2-yl]oxy}butanenitrile C₃₁ H₄₉ N O₄ KQWXEWOYVIUCOD-IBOBMRDDSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free: 0.217 (Depositor), 0.225 (DCC)
R-Value Work: 0.190 (Depositor), 0.199 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.663	α = 90
b = 51.842	β = 90
c = 131.475	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-11-09

Deposition Author(s):

Takimoto-Kamimura, M.

This entry supersedes: 4PA2

Revision History (Full details and data files)

Version 1.0: 2016-11-09
Type: Initial release
Version 1.1: 2020-02-26
Changes: Data collection, Derived calculations
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.