5VQK | pdb_00005vqk

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/pdb5VQK/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: 3.10 Å
R-Value Free:
0.246 (Depositor), 0.230 (DCC)
R-Value Work:
0.194 (Depositor), 0.200 (DCC)
R-Value Observed:
0.196 (Depositor)

wwPDB Validation 3D Report Full Report

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: 32.91 kDa
Atom Count: 2,075
Modeled Residue Count: 256
Deposited Residue Count: 280
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P51449Q15596
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9GV Query on 9GV 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]	1-(4-fluorophenyl)-7-methoxy-N-{[4-(methylsulfamoyl)phenyl]methyl}-1H-pyrazolo[3,4-c]pyridine-4-carboxamide C₂₂ H₂₀ F N₅ O₄ S XCGQNCJLJMSYMR-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
9GV	BindingDB: 5VQK	IC50: 1600 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.246 (Depositor), 0.230 (DCC)
R-Value Work: 0.194 (Depositor), 0.200 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.725	α = 90
b = 64.725	β = 90
c = 159.322	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

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 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.