5k3m

Crystal structure of Retinoic acid receptor-related orphan receptor (ROR) gamma ligand binding domain complex with UUA

Method: X-RAY DIFFRACTION Dmax: 76.5 Å Quality: EXCELLENT

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 244–486 Fragment:ligand binding domain 6Q5 Ursolic acid × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;289 K;0.4M Potassium sodium tartrate tetrahydrate Resolution 2.89 Å R-free 0.295
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 244–486 Fragment:ligand binding domain 6Q5 Ursolic acid × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;289 K;0.4M Potassium sodium tartrate tetrahydrate Resolution 2.89 Å R-free 0.295

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 P51449-2
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 5–247; UniProt 244–486 Author chain B; PDBConstruct 5–247; UniProt 244–486

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 5k3m

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5k3m
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5k3m
Deposition date deposition_date2016-05-19
Structure title titleCrystal structure of Retinoic acid receptor-related orphan receptor (ROR) gamma ligand binding domain complex with UUA
Keywords keywordsdouble helix, PROTEIN BINDING; PROTEIN BINDING
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier26.11
Radius of gyration Rg (electron density) rg_electron24.87
Forward intensity I(0) i045241000.00
Molecular weight molecular_weight52581.0 kDa
Excluded volume excluded_volume66152 ų
Envelope volume envelope_volume84016 ų
Hydration-shell volume shell_volume27910 ų
Envelope diameter envelope_diameter79.0
Shell Rg shell_rg32.06
Envelope Rg envelope_rg24.57
Shape Rg shape_rg24.86
Total Rg total_rg25.75
Total atoms total_atoms3692
Residues n_residues444
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 dmax76.5
Rg (real space) rg_real25.96
Rg uncertainty (real space) rg_real_error0.40
I(0) (real space) i0_real4.5240e+07
I(0) uncertainty (real space) i0_real_error5.6340e+05
Rg (reciprocal space) rg_reciprocal26.01
I(0) (reciprocal space) i0_reciprocal45240000.0000
Solution quality estimate total_estimate0.9168
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary31.3
Skewness Skewness skewness0.075
Kurtosis Kurtosis kurtosis-0.701
Angular range angular_range— – 0.3050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7441000.0000
Real-space data points n_real_points62
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.983; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.970

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd5k3ma_
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_idd5k3mb_
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_id5k3mA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology565 — Retinoid X Receptor
Homologous superfamily homologous superfamily10 — Retinoid X Receptor
Domain ID domain_id5k3mB00
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)