5ayg

Crystal Structure of the Human ROR gamma Ligand Binding Domain With 3g

Method: X-RAY DIFFRACTION Dmax: 83.4 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 261–518 Fragment:UNP residues 261-518 4LQ 3-[5-(2-cyclohexylethyl)-4-ethyl-1,2,4-triazol-3-yl]-N-naphthalen-1-yl-propanamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;293 K;0.1M Tris-HCl , pH 7.5, 0.5M Na/K tartrate, 2.5M, MPD Resolution 2.60 Å R-free 0.227
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 261–518 Fragment:UNP residues 261-518 4LQ 3-[5-(2-cyclohexylethyl)-4-ethyl-1,2,4-triazol-3-yl]-N-naphthalen-1-yl-propanamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;293 K;0.1M Tris-HCl , pH 7.5, 0.5M Na/K tartrate, 2.5M, MPD Resolution 2.60 Å R-free 0.227

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 1–258; UniProt 261–518 Author chain B; PDBConstruct 1–258; UniProt 261–518

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 5ayg

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id5ayg
Deposition date deposition_date2015-08-20
Structure title titleCrystal Structure of the Human ROR gamma Ligand Binding Domain With 3g
Keywords keywordsInhibitor, Complex, Nuclear Receptor, DNA BINDING PROTEIN-INHIBITOR complex; DNA BINDING PROTEIN/INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier26.88
Radius of gyration Rg (electron density) rg_electron25.65
Forward intensity I(0) i043384900.00
Molecular weight molecular_weight50874.0 kDa
Excluded volume excluded_volume63729 ų
Envelope volume envelope_volume82426 ų
Hydration-shell volume shell_volume26778 ų
Envelope diameter envelope_diameter86.6
Shell Rg shell_rg32.81
Envelope Rg envelope_rg25.23
Shape Rg shape_rg25.66
Total Rg total_rg26.46
Total atoms total_atoms3572
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 dmax83.4
Rg (real space) rg_real26.76
Rg uncertainty (real space) rg_real_error0.42
I(0) (real space) i0_real4.3380e+07
I(0) uncertainty (real space) i0_real_error4.9890e+05
Rg (reciprocal space) rg_reciprocal26.80
I(0) (reciprocal space) i0_reciprocal43390000.0000
Solution quality estimate total_estimate0.9075
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary38.1
Skewness Skewness skewness0.100
Kurtosis Kurtosis kurtosis-0.669
Angular range angular_range— – 0.2950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9283000.0000
Real-space data points n_real_points60
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.947; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.955

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_idd5ayga_
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_idd5aygb_
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_id5aygA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology565 — Retinoid X Receptor
Homologous superfamily homologous superfamily10 — Retinoid X Receptor
Domain ID domain_id5aygB00
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)