6q2w

Crystal structure of human ROR gamma LBD in complex with a quinoline sulfonamide inverse agonist

Method: X-RAY DIFFRACTION Dmax: 85.8 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

Nuclear receptor ROR-gamma

Homo sapiens

UniProt P51449

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 267–487 Not recorded HBW (2~{S})-1-[2,4-bis(chloranyl)-3-[[4-imidazol-1-yl-2-(trifluoromethyl)quinolin-8-yl]oxymethyl]phenyl]sulfonyl-~{N}-methyl-pyrrolidine-2-carboxamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;277 K;0.1M MgCl2, 0.1M Mes pH 6, 8% w/v PEG 6000 Resolution 1.99 Å R-free 0.232
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 267–487 Not recorded HBW (2~{S})-1-[2,4-bis(chloranyl)-3-[[4-imidazol-1-yl-2-(trifluoromethyl)quinolin-8-yl]oxymethyl]phenyl]sulfonyl-~{N}-methyl-pyrrolidine-2-carboxamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;277 K;0.1M MgCl2, 0.1M Mes pH 6, 8% w/v PEG 6000 Resolution 1.99 Å R-free 0.232

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

161 other PDB entries and 266 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RORG_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–221; UniProt 267–487 Author chain B; PDBConstruct 1–221; UniProt 267–487

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 6q2w

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6q2w
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6q2w
Deposition date deposition_date2018-12-03
Structure title titleCrystal structure of human ROR gamma LBD in complex with a quinoline sulfonamide inverse agonist
Keywords keywordsROR gamma, inverse agonist, nuclear hormone receptor, transcription; TRANSCRIPTION
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier25.97
Radius of gyration Rg (electron density) rg_electron24.95
Forward intensity I(0) i046092800.00
Molecular weight molecular_weight52100.0 kDa
Excluded volume excluded_volume65011 ų
Envelope volume envelope_volume78658 ų
Hydration-shell volume shell_volume26546 ų
Envelope diameter envelope_diameter89.8
Shell Rg shell_rg31.88
Envelope Rg envelope_rg25.15
Shape Rg shape_rg24.96
Total Rg total_rg25.69
Total atoms total_atoms3651
Residues n_residues441
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax85.8
Rg (real space) rg_real25.97
Rg uncertainty (real space) rg_real_error0.56
I(0) (real space) i0_real4.6090e+07
I(0) uncertainty (real space) i0_real_error6.5460e+05
Rg (reciprocal space) rg_reciprocal25.97
I(0) (reciprocal space) i0_reciprocal46090000.0000
Solution quality estimate total_estimate0.8910
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.7
Skewness Skewness skewness0.314
Kurtosis Kurtosis kurtosis-0.458
Angular range angular_range— – 0.3050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha14200000.0000
Real-space data points n_real_points62
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.879; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.962

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd6q2wa_
Class classa — All alpha proteins
Fold Fold folda.123 — Nuclear receptor ligand-binding domain
Superfamily Superfamily superfamilya.123.1 — Nuclear receptor ligand-binding domain
Family Family familya.123.1.0 — automated matches
Domain ID domain_idd6q2wb_
Class classa — All alpha proteins
Fold Fold folda.123 — Nuclear receptor ligand-binding domain
Superfamily Superfamily superfamilya.123.1 — Nuclear receptor ligand-binding domain
Family Family familya.123.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id6q2wA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology565 — Retinoid X Receptor
Homologous superfamily homologous superfamily10 — Retinoid X Receptor
Domain ID domain_id6q2wB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology565 — Retinoid X Receptor
Homologous superfamily homologous superfamily10 — Retinoid X Receptor

8. Citations (1)

9. Files and Curves (10)