5K3L | pdb_00005k3l

Crystal structure of Retinoic acid receptor-related orphan receptor (ROR) gamma ligand binding domain complex with 444

• PDB DOI: https://doi.org/10.2210/pdb5K3L/pdb

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


• Deposited: 2016-05-19 Released: 2017-05-31 
• Deposition Author(s): Huang, P., Rastinejad, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.264 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.242 (Depositor) 

Literature

Crystal structure of Retinoic acid receptor-related orphan receptor (ROR) gamma ligand binding domain complex with 444

Lu, J., Rastinejad, F.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 116.81 kDa 
• Atom Count: 7,516 
• Modeled Residue Count: 903 
• Deposited Residue Count: 988 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor ROR-gamma	A, B, C, D	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
444	E [auth A], F [auth B], G [auth C], H [auth D]	N-(2,2,2-TRIFLUOROETHYL)-N-{4-[2,2,2-TRIFLUORO-1-HYDROXY-1-(TRIFLUOROMETHYL)ETHYL]PHENYL}BENZENESULFONAMIDE C17 H12 F9 N O3 S SGIWFELWJPNFDH-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
444	BindingDB:  5K3L	Ki: 51 (nM) from 1 assay(s)
		IC50: min: 60, max: 6500 (nM) from 14 assay(s)
		EC50: min: 54, max: 463 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.264 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.239 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.242 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.558	α = 90
b = 89.558	β = 90
c = 153.286	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data collection
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-31 
Deposition Author(s): Huang, P., Rastinejad, F.

Revision History  

• Version 1.0: 2017-05-31
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references