5ntk

Structural states of RORgt: X-ray elucidation of molecular mechanisms and binding interactions for natural and synthetic compounds

Method: X-RAY DIFFRACTION Dmax: 87.4 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 263–491 Fragment:C-terminal domain, ligand binding domain Mutation:C455S 99N [(3~{S},8~{S},9~{S},10~{R},13~{R},14~{S},17~{R})-10,13-dimethyl-17-[(2~{R})-5-[[4-(2-morpholin-4-ylethoxy)phenyl]methylamino]-5-oxidanylidene-pentan-2-yl]-2,3,4,7,8,9,11,12,14,15,16,17-dodecahydro-1~{H}-cyclopenta[a]phenanthren-3-yl] hydrogen sulfate × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;298 K;20% PEG 3350, 0.1M MES Resolution 1.90 Å R-free 0.246
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 263–491 Fragment:C-terminal domain, ligand binding domain Mutation:C455S 99N [(3~{S},8~{S},9~{S},10~{R},13~{R},14~{S},17~{R})-10,13-dimethyl-17-[(2~{R})-5-[[4-(2-morpholin-4-ylethoxy)phenyl]methylamino]-5-oxidanylidene-pentan-2-yl]-2,3,4,7,8,9,11,12,14,15,16,17-dodecahydro-1~{H}-cyclopenta[a]phenanthren-3-yl] hydrogen sulfate × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;298 K;20% PEG 3350, 0.1M MES Resolution 1.90 Å R-free 0.246

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 2–230; UniProt 263–491 Author chain B; PDBConstruct 2–230; UniProt 263–491

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 5ntk

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5ntk
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5ntk
Deposition date deposition_date2017-04-28
Structure title titleStructural states of RORgt: X-ray elucidation of molecular mechanisms and binding interactions for natural and synthetic compounds
Keywords keywordsnuclear hormone receptor, ligand-binding domain, inverse agonist, NUCLEAR PROTEIN; NUCLEAR PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier26.81
Radius of gyration Rg (electron density) rg_electron26.01
Forward intensity I(0) i047344600.00
Molecular weight molecular_weight53739.0 kDa
Excluded volume excluded_volume67494 ų
Envelope volume envelope_volume82992 ų
Hydration-shell volume shell_volume27148 ų
Envelope diameter envelope_diameter91.2
Shell Rg shell_rg32.71
Envelope Rg envelope_rg26.01
Shape Rg shape_rg25.99
Total Rg total_rg26.82
Total atoms total_atoms3774
Residues n_residues450
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 dmax87.4
Rg (real space) rg_real26.82
Rg uncertainty (real space) rg_real_error0.60
I(0) (real space) i0_real4.7340e+07
I(0) uncertainty (real space) i0_real_error6.6290e+05
Rg (reciprocal space) rg_reciprocal26.82
I(0) (reciprocal space) i0_reciprocal47340000.0000
Solution quality estimate total_estimate0.8920
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.7
Skewness Skewness skewness0.337
Kurtosis Kurtosis kurtosis-0.463
Angular range angular_range— – 0.2950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha14640000.0000
Real-space data points n_real_points60
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.890; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.958; Smooth: 0.965

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_idd5ntka_
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_idd5ntkb_
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_id5ntkA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology565 — Retinoid X Receptor
Homologous superfamily homologous superfamily10 — Retinoid X Receptor
Domain ID domain_id5ntkB00
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)