8fb1

HUMAN RETENOID-RELATED ORPHAN RECEPTOR-GAMMA (RORC2) LIGAND-BINDING DOMAIN IN COMPLEX WITH COMPOUND 6a ANDINDAZOLE ACID BOUND IN H12-POCKET

Method: X-RAY DIFFRACTION Dmax: 111.6 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 259–517 Mutation:C278S, C345S XNR N-(3-{[(3S)-4-(cyclopentanecarbonyl)-3-methylpiperazin-1-yl]methyl}-5-fluoro-2-methylphenyl)-4-fluorobenzene-1-sulfonamide × 1 4Y5 4-{1-[2-chloro-6-(trifluoromethyl)benzoyl]-4-fluoro-1H-indazol-3-yl}-3-fluorobenzoic acid × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;298 K;100 mM MES pH 5.9, 5 mM ammonium sulfate, 300 mM magnesium chloride, 10% N,N-dimethylformamide, and 14% PEG-MME-5000 Resolution 2.18 Å R-free 0.253
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 259–517 Mutation:C278S, C345S XNR N-(3-{[(3S)-4-(cyclopentanecarbonyl)-3-methylpiperazin-1-yl]methyl}-5-fluoro-2-methylphenyl)-4-fluorobenzene-1-sulfonamide × 1 4Y5 4-{1-[2-chloro-6-(trifluoromethyl)benzoyl]-4-fluoro-1H-indazol-3-yl}-3-fluorobenzoic acid × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;298 K;100 mM MES pH 5.9, 5 mM ammonium sulfate, 300 mM magnesium chloride, 10% N,N-dimethylformamide, and 14% PEG-MME-5000 Resolution 2.18 Å R-free 0.253

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 4–262; UniProt 259–517 Author chain B; PDBConstruct 4–262; UniProt 259–517

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 8fb1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8fb1
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8fb1
Deposition date deposition_date2022-11-29
Structure title titleHUMAN RETENOID-RELATED ORPHAN RECEPTOR-GAMMA (RORC2) LIGAND-BINDING DOMAIN IN COMPLEX WITH COMPOUND 6a ANDINDAZOLE ACID BOUND IN H12-POCKET
Keywords keywordsRORC2, RORgammat, structure-based design, macrocyclization, topical delivery, DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier32.10
Radius of gyration Rg (electron density) rg_electron32.04
Forward intensity I(0) i056547600.00
Molecular weight molecular_weight59976.0 kDa
Excluded volume excluded_volume75207 ų
Envelope volume envelope_volume94599 ų
Hydration-shell volume shell_volume27031 ų
Envelope diameter envelope_diameter112.1
Shell Rg shell_rg35.54
Envelope Rg envelope_rg32.08
Shape Rg shape_rg32.04
Total Rg total_rg32.35
Total atoms total_atoms4219
Residues n_residues496
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 dmax111.6
Rg (real space) rg_real32.56
Rg uncertainty (real space) rg_real_error1.23
I(0) (real space) i0_real5.6550e+07
I(0) uncertainty (real space) i0_real_error1.0460e+06
Rg (reciprocal space) rg_reciprocal32.37
I(0) (reciprocal space) i0_reciprocal56540000.0000
Solution quality estimate total_estimate0.7607
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.1
Skewness Skewness skewness0.538
Kurtosis Kurtosis kurtosis-0.533
Angular range angular_range— – 0.2450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha19180000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.520; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.507; Smooth: 0.818

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (1)

9. Files and Curves (10)