5nib

Ligand complex of RORg LBD

Method: X-RAY DIFFRACTION Dmax: 68.8 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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 265–507 Not recorded The tethered SRC2-2 peptide × 1 8Y5 ~{N}-[4-[2-[(3-cyanophenyl)methoxy]pyridin-3-yl]thiophen-2-yl]-2-(4-ethylsulfonylphenyl)ethanamide × 1 NA SODIUM ION × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;295 K;0.1M Bis tris pH 6.25, 0.1 M NaCl, 2M NaFormate Resolution 1.82 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 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 23–265; 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 5nib

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id5nib
Deposition date deposition_date2017-03-23
Structure title titleLigand complex of RORg LBD
Keywords keywordsRAR-related Orphan Receptor-g (RORg), TRANSCRIPTION, RORG LIGAND, STRUCTURE-BASED DESIGN; RAR-related Orphan Receptor-g (RORg)
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier20.21
Radius of gyration Rg (electron density) rg_electron18.96
Forward intensity I(0) i016630600.00
Molecular weight molecular_weight31041.0 kDa
Excluded volume excluded_volume38980 ų
Envelope volume envelope_volume44851 ų
Hydration-shell volume shell_volume19832 ų
Envelope diameter envelope_diameter66.9
Shell Rg shell_rg25.28
Envelope Rg envelope_rg19.19
Shape Rg shape_rg18.96
Total Rg total_rg19.86
Total atoms total_atoms2181
Residues n_residues262
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 dmax68.8
Rg (real space) rg_real20.13
Rg uncertainty (real space) rg_real_error0.51
I(0) (real space) i0_real1.6630e+07
I(0) uncertainty (real space) i0_real_error2.2850e+05
Rg (reciprocal space) rg_reciprocal20.15
I(0) (reciprocal space) i0_reciprocal16630000.0000
Solution quality estimate total_estimate0.8715
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.5
Skewness Skewness skewness0.253
Kurtosis Kurtosis kurtosis-0.309
Angular range angular_range— – 0.3950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3853000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.780; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.991

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd5niba1
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_idd5niba2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd5niba3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id5nibA00
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)