6slz

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

Method: X-RAY DIFFRACTION Dmax: 85.0 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 261–507 Not recorded LK8 (2~{S})-1-[2,4-bis(chloranyl)-3-[[2-methyl-4-(trifluoromethyl)quinolin-8-yl]oxymethyl]phenyl]carbonyl-~{N}-methyl-pyrrolidine-2-carboxamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;295 K;0.2M NH4 formate, 20% w/v PEG 3350 Resolution 2.20 Å R-free 0.278
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 261–507 Not recorded LK8 (2~{S})-1-[2,4-bis(chloranyl)-3-[[2-methyl-4-(trifluoromethyl)quinolin-8-yl]oxymethyl]phenyl]carbonyl-~{N}-methyl-pyrrolidine-2-carboxamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;295 K;0.2M NH4 formate, 20% w/v PEG 3350 Resolution 2.20 Å R-free 0.278

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 1–247; UniProt 261–507 Author chain B; PDBConstruct 1–247; UniProt 261–507

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 6slz

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6slz
Deposition date deposition_date2019-08-21
Structure title titleCrystal structure of human ROR gamma LBD in complex with a (quinolinoxymethyl)benzamide inverse agonist
Keywords keywordsRORg, 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_guinier25.85
Radius of gyration Rg (electron density) rg_electron24.71
Forward intensity I(0) i044856200.00
Molecular weight molecular_weight51479.0 kDa
Excluded volume excluded_volume64315 ų
Envelope volume envelope_volume78022 ų
Hydration-shell volume shell_volume26668 ų
Envelope diameter envelope_diameter89.6
Shell Rg shell_rg31.58
Envelope Rg envelope_rg24.77
Shape Rg shape_rg24.72
Total Rg total_rg25.47
Total atoms total_atoms3610
Residues n_residues436
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 dmax85.0
Rg (real space) rg_real25.82
Rg uncertainty (real space) rg_real_error0.51
I(0) (real space) i0_real4.4860e+07
I(0) uncertainty (real space) i0_real_error5.9220e+05
Rg (reciprocal space) rg_reciprocal25.83
I(0) (reciprocal space) i0_reciprocal44860000.0000
Solution quality estimate total_estimate0.8937
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.9
Skewness Skewness skewness0.297
Kurtosis Kurtosis kurtosis-0.469
Angular range angular_range— – 0.3050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11920000.0000
Real-space data points n_real_points62
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.888; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.962

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd6slza_
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_idd6slzb_
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

8. Citations (1)

9. Files and Curves (10)