6t4k

ROR(gamma)t ligand binding domain in complex with desmosterol and allosteric ligand MRL871

Method: X-RAY DIFFRACTION Dmax: 63.9 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 265–507 Not recorded MHQ desmosterol × 1 4F1 4-{1-[2-chloro-6-(trifluoromethyl)benzoyl]-1H-indazol-3-yl}benzoic acid × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;293 K;0.2 M MgCl2 + 6% PEG6K + 0.1M Tris Resolution 1.89 Å R-free 0.205

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 267 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 21–263; UniProt 265–507

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 6t4k

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6t4k
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6t4k
Deposition date deposition_date2019-10-14
Structure title titleROR(gamma)t ligand binding domain in complex with desmosterol and allosteric ligand MRL871
Keywords keywordsNuclear Receptor, Allosteric, Inverse Agonist, Inhibitor, GENE REGULATION; GENE REGULATION
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier19.67
Radius of gyration Rg (electron density) rg_electron18.31
Forward intensity I(0) i014331800.00
Molecular weight molecular_weight29070.0 kDa
Excluded volume excluded_volume36678 ų
Envelope volume envelope_volume41371 ų
Hydration-shell volume shell_volume18921 ų
Envelope diameter envelope_diameter66.4
Shell Rg shell_rg24.56
Envelope Rg envelope_rg18.58
Shape Rg shape_rg18.32
Total Rg total_rg19.24
Total atoms total_atoms2045
Residues n_residues240
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 dmax63.9
Rg (real space) rg_real19.58
Rg uncertainty (real space) rg_real_error0.38
I(0) (real space) i0_real1.4330e+07
I(0) uncertainty (real space) i0_real_error1.7850e+05
Rg (reciprocal space) rg_reciprocal19.59
I(0) (reciprocal space) i0_reciprocal14330000.0000
Solution quality estimate total_estimate0.8089
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.2
Skewness Skewness skewness0.236
Kurtosis Kurtosis kurtosis-0.287
Angular range angular_range— – 0.4050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2533000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.838; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd6t4ka_
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)