6SLZ | pdb_00006slz

Crystal structure of human ROR gamma LBD in complex with a (quinolinoxymethyl)benzamide inverse agonist

• PDB DOI: https://doi.org/10.2210/pdb6SLZ/pdb

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


• Deposited: 2019-08-21 Released: 2020-09-09 
• Deposition Author(s): Amaudrut, J., Argiriadi, M.A., Barth, M., Breinlinger, E.C., Calderwood, D.J., Cusack, K.P., Kort, M.E., Montalbetti, C., Potin, D., Poupardin, O., Spitzer, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.278 (Depositor), 0.281 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human ROR gamma LBD in complex with a (quinolinoxymethyl)benzamide inverse agonist

Amaudrut, J., Argiriadi, M.A., Barth, M., Breinlinger, E.C., Calderwood, D.J., Cusack, K.P., Kort, M.E., Montalbetti, C., Potin, D., Poupardin, O., Spitzer, L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 58.52 kDa 
• Atom Count: 3,781 
• Modeled Residue Count: 436 
• Deposited Residue Count: 494 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor ROR-gamma	A, B	247	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LK8 (Subject of Investigation/LOI)	C [auth A], D [auth B]	(2~{S})-1-[2,4-bis(chloranyl)-3-[[2-methyl-4-(trifluoromethyl)quinolin-8-yl]oxymethyl]phenyl]carbonyl-~{N}-methyl-pyrrolidine-2-carboxamide C25 H22 Cl2 F3 N3 O3 SGDYSAAUPQPUSM-IBGZPJMESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.278 (Depositor), 0.281 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.67	α = 90
b = 56.33	β = 124.76
c = 80.92	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-09-09 
Deposition Author(s): Amaudrut, J., Argiriadi, M.A., Barth, M., Breinlinger, E.C., Calderwood, D.J., Cusack, K.P., Kort, M.E., Montalbetti, C., Potin, D., Poupardin, O., Spitzer, L.

Revision History  

• Version 1.0: 2020-09-09
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description