5VQL | pdb_00005vql

X-ray co-structure of nuclear receptor ROR-gammat Ligand Binding Domain with a inverse agonist and SRC2 peptide

PDB DOI: https://doi.org/10.2210/pdb5VQL/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-05-09 Released: 2018-05-16
Deposition Author(s): Li, X.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.251 (Depositor), 0.259 (DCC)
R-Value Work:
0.218 (Depositor), 0.224 (DCC)
R-Value Observed:
0.220 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5VQL

Ligand Structure Quality Assessment

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

Literature

X-ray co-structure of nuclear receptor ROR-gammat Ligand Binding Domain with a inverse agonist and SRC2 peptide

Li, X.

To be published.

Macromolecule Content

Total Structure Weight: 33.01 kDa
Atom Count: 2,181
Modeled Residue Count: 259
Deposited Residue Count: 280
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor ROR-gamma, SRC2 chimera	A	280	Homo sapiens	Mutation(s): 0 Gene Names: RORC, NR1F3, RORG, RZRG
UniProt & NIH Common Fund Data Resources
Find proteins for P51449 (Homo sapiens) Explore P51449 Go to UniProtKB: P51449
PHAROS: P51449 GTEx: ENSG00000143365
Find proteins for Q15596 (Homo sapiens) Explore Q15596 Go to UniProtKB: Q15596
PHAROS: Q15596 GTEx: ENSG00000140396
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	P51449 Q15596
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9GS Query on 9GS 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]	5'-(4-cyclopropyl-6-methoxypyrimidin-5-yl)-N-{[4-(ethylsulfonyl)phenyl]methyl}spiro[cyclopentane-1,3'-pyrrolo[3,2-b]pyridine]-1'(2'H)-carboxamide C₂₉ H₃₃ N₅ O₄ S PWIXSNKHPMGRRW-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
NA Query on NA 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]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.251 (Depositor), 0.259 (DCC)
R-Value Work: 0.218 (Depositor), 0.224 (DCC)
R-Value Observed: 0.220 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.325	α = 90
b = 61.325	β = 90
c = 155.578	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
d*TREK	data reduction
d*TREK	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2018-05-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-05-16
Type: Initial release
Version 1.1: 2024-03-13
Changes: Data collection, Database references

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.