6b31

Structure of RORgt in complex with a novel inverse agonist 2

Method: X-RAY DIFFRACTION Dmax: 86.0 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 265–492 Not recorded CFJ (3S)-N~1~-(3-chloro-4-cyanophenyl)-N~5~-(1,3-diethyl-2,4-dioxo-1,2,3,4-tetrahydroquinazolin-6-yl)-3-methylpentanediamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;291 K;1.6M Sodium Formate, 3% MPD, and 100 mM HEPES (pH 7.5) Resolution 3.18 Å R-free 0.245
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 265–492 Not recorded CFJ (3S)-N~1~-(3-chloro-4-cyanophenyl)-N~5~-(1,3-diethyl-2,4-dioxo-1,2,3,4-tetrahydroquinazolin-6-yl)-3-methylpentanediamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;291 K;1.6M Sodium Formate, 3% MPD, and 100 mM HEPES (pH 7.5) Resolution 3.18 Å R-free 0.245

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 1–228; UniProt 265–492 Author chain B; PDBConstruct 1–228; UniProt 265–492

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 6b31

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6b31
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6b31
Deposition date deposition_date2017-09-20
Structure title titleStructure of RORgt in complex with a novel inverse agonist 2
Keywords keywordsComplex, inverse agonist, Nuclear Hormone Receptor, SIGNALING PROTEIN, signaling protein-agonist complex; signaling protein/agonist
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier26.26
Radius of gyration Rg (electron density) rg_electron25.19
Forward intensity I(0) i049017300.00
Molecular weight molecular_weight53998.0 kDa
Excluded volume excluded_volume67512 ų
Envelope volume envelope_volume83763 ų
Hydration-shell volume shell_volume27891 ų
Envelope diameter envelope_diameter89.6
Shell Rg shell_rg32.25
Envelope Rg envelope_rg25.16
Shape Rg shape_rg25.18
Total Rg total_rg26.01
Total atoms total_atoms3792
Residues n_residues455
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 dmax86.0
Rg (real space) rg_real26.19
Rg uncertainty (real space) rg_real_error0.72
I(0) (real space) i0_real4.9020e+07
I(0) uncertainty (real space) i0_real_error7.3020e+05
Rg (reciprocal space) rg_reciprocal26.22
I(0) (reciprocal space) i0_reciprocal49020000.0000
Solution quality estimate total_estimate0.8986
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.7
Skewness Skewness skewness0.245
Kurtosis Kurtosis kurtosis-0.452
Angular range angular_range— – 0.3000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9395000.0000
Real-space data points n_real_points61
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.896; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.994

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_idd6b31a_
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_idd6b31b_
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_id6b31A00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology565 — Retinoid X Receptor
Homologous superfamily homologous superfamily10 — Retinoid X Receptor
Domain ID domain_id6b31B00
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)