5g42

Ligand complex of RORg LBD

Method: X-RAY DIFFRACTION Dmax: 66.4 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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 265–507 Fragment:LIGAND BINDING DOMAIN, RESIDUES 265-507 RORG × 1 4TU 5-chloranyl-2,3-dihydroindole-1-carboxamide × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 1.72 Å R-free 0.212

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 22–264; 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 5g42

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5g42
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id5g42
Deposition date deposition_date2016-05-04
Structure title titleLigand complex of RORg LBD
Keywords keywordsDNA BINDING PROTEIN, RORG LIGAND, FRAGMENT SCREEN, STRUCTURE-BASED DESIGN, SIMULTANEOUS BINDING; DNA BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier20.28
Radius of gyration Rg (electron density) rg_electron19.04
Forward intensity I(0) i016290100.00
Molecular weight molecular_weight30642.0 kDa
Excluded volume excluded_volume38470 ų
Envelope volume envelope_volume44619 ų
Hydration-shell volume shell_volume19765 ų
Envelope diameter envelope_diameter66.1
Shell Rg shell_rg25.22
Envelope Rg envelope_rg19.15
Shape Rg shape_rg19.04
Total Rg total_rg19.92
Total atoms total_atoms2154
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 dmax66.4
Rg (real space) rg_real20.20
Rg uncertainty (real space) rg_real_error0.37
I(0) (real space) i0_real1.6290e+07
I(0) uncertainty (real space) i0_real_error2.0190e+05
Rg (reciprocal space) rg_reciprocal20.21
I(0) (reciprocal space) i0_reciprocal16290000.0000
Solution quality estimate total_estimate0.8866
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.7
Skewness Skewness skewness0.234
Kurtosis Kurtosis kurtosis-0.338
Angular range angular_range— – 0.3900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3212000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.852; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.967

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd5g42a1
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_idd5g42a2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd5g42a3
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_id5g42A00
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)