245,778
Structures from the PDB archive

1,068,577
Computed Structure Models (CSM)

3WTQ|pdb_00003wtq

Crystal structure of VDR-LBD complexed with 22S-butyl-2-methylidene-19-nor-1a,25-dihydroxyvitamin D3

PDB DOI: https://doi.org/10.2210/pdb3WTQ/pdb

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

Deposited: 2014-04-15 Released: 2015-04-15
Deposition Author(s): Nakabayashi, M.,Inaba, Y.,Itoh, T.,Anami, Y.,Ikura, T.,Ito, N.,Yamamoto, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.275 (Depositor), 0.280 (DCC)
R-Value Work:
0.232 (Depositor), 0.230 (DCC)
R-Value Observed:
0.234 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of VDR-LBD complexed with 22S-butyl-2-methylidene-19-nor-1a,25-dihydroxyvitamin D3

Nakabayashi, M., Inaba, Y., Itoh, T., Anami, Y., Ikura, T., Ito, N., Yamamoto, K.

To be published.

Macromolecule Content

Total Structure Weight: 32.64 kDa
Atom Count: 2,159
Modeled Residue Count: 251
Deposited Residue Count: 284
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vitamin D3 receptor	A	271	Rattus norvegicus	Mutation(s): 0 Gene Names: Vdr, Nr1i1
UniProt
Find proteins for P13053 (Rattus norvegicus) Explore P13053 Go to UniProtKB: P13053
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P13053
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Mediator of RNA polymerase II transcription subunit 1	B [auth C]	13	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q15648 (Homo sapiens) Explore Q15648 Go to UniProtKB: Q15648
PHAROS: Q15648 GTEx: ENSG00000125686
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q15648
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YS9 Query on YS9 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]	(1R,3R,7E,17beta)-17-[(2R,3S)-3-butyl-6-hydroxy-6-methylheptan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol C₃₁ H₅₂ O₃ RSXHMKSDJHHTDU-VWOHJUMJSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.275 (Depositor), 0.280 (DCC)
R-Value Work: 0.232 (Depositor), 0.230 (DCC)
R-Value Observed: 0.234 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.286	α = 90
b = 43.851	β = 96.18
c = 42.321	γ = 90

Software Package:

Software Name	Purpose
SERGUI	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2015-04-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-04-15
Type: Initial release
Version 1.1: 2015-08-05
Changes: Database references, Structure summary
Version 1.2: 2017-11-22
Changes: Refinement description
Version 1.3: 2024-03-20
Changes: Data collection, Database references, Derived calculations