7WQQ | pdb_00007wqq

Retinoic acid receptor alpha mutant - N299H

PDB DOI: https://doi.org/10.2210/pdb7WQQ/pdb

Classification: GENE REGULATION
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2022-01-25 Released: 2023-01-25
Deposition Author(s): Huang, X.X., Ng, L.M., Teh, B.T.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.206 (Depositor), 0.205 (DCC)
R-Value Work:
0.166 (Depositor), 0.166 (DCC)
R-Value Observed:
0.170 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Effects of breast fibroepithelial tumor associated retinoic acid receptor alpha ligand binding domain mutations on receptor function and retinoid signaling

Huang, X.X., Ng, L.M., Teh, B.T.

To be published.

Macromolecule Content

Total Structure Weight: 32.11 kDa
Atom Count: 2,060
Modeled Residue Count: 237
Deposited Residue Count: 278
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinoic acid receptor alpha	A	265	Homo sapiens	Mutation(s): 1 Gene Names: RARA, NR1B1
UniProt & NIH Common Fund Data Resources
Find proteins for P10276 (Homo sapiens) Explore P10276 Go to UniProtKB: P10276
PHAROS: P10276 GTEx: ENSG00000131759
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P10276
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide from Nuclear receptor coactivator 1	B [auth C]	13	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
5Z6 (Subject of Investigation/LOI) Query on 5Z6 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]	4-[(E)-3-(3,5-ditert-butylphenyl)-3-oxidanylidene-prop-1-enyl]benzoic acid C₂₄ H₂₈ O₃ FOUVTBKPJRMLPE-FMIVXFBMSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.206 (Depositor), 0.205 (DCC)
R-Value Work: 0.166 (Depositor), 0.166 (DCC)
R-Value Observed: 0.170 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.915	α = 90
b = 64.979	β = 105.23
c = 49.205	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-01-25

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	Singapore	OFIRG16may055

Revision History (Full details and data files)

Version 1.0: 2023-01-25
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, 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.