6cn5

HUMAN RETENOID-RELATED ORPHAN RECEPTOR-GAMMA LIGAND- BINDING DOMAIN IN COMPLEX WITH INDOLE LIGAND CP9b IN INVERSE AGONIST CONFORMATION

Method: X-RAY DIFFRACTION Dmax: 81.1 Å Quality: REASONABLE

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 259–518 Fragment:ligand binding domain F7M 4-cyano-N-{3-[1-(cyclohexanecarbonyl)piperidin-4-yl]-1-methyl-1H-indol-5-yl}pyridine-2-carboxamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 7.5;298 K;1.8-2.5M Na formate, 0.1 MTris-HCl pH 7.5-8.0, 3% methyl pentane diol Resolution 2.30 Å R-free 0.222
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 259–518 Fragment:ligand binding domain F7M 4-cyano-N-{3-[1-(cyclohexanecarbonyl)piperidin-4-yl]-1-methyl-1H-indol-5-yl}pyridine-2-carboxamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 7.5;298 K;1.8-2.5M Na formate, 0.1 MTris-HCl pH 7.5-8.0, 3% methyl pentane diol Resolution 2.30 Å R-free 0.222

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 3–262; UniProt 259–518 Author chain B; PDBConstruct 3–262; UniProt 259–518

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 6cn5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6cn5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6cn5
Deposition date deposition_date2018-03-07
Structure title titleHUMAN RETENOID-RELATED ORPHAN RECEPTOR-GAMMA LIGAND- BINDING DOMAIN IN COMPLEX WITH INDOLE LIGAND CP9b IN INVERSE AGONIST CONFORMATION
Keywords keywordsROR GAMMA, LIGAND-BINDING, NUCLEAR RECEPTOR, NON STEROIDAL, INDOLE, PFIZER, INVERSE AGONIST, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier27.51
Radius of gyration Rg (electron density) rg_electron26.47
Forward intensity I(0) i049326900.00
Molecular weight molecular_weight54712.0 kDa
Excluded volume excluded_volume68601 ų
Envelope volume envelope_volume88807 ų
Hydration-shell volume shell_volume27658 ų
Envelope diameter envelope_diameter82.5
Shell Rg shell_rg34.06
Envelope Rg envelope_rg26.09
Shape Rg shape_rg26.45
Total Rg total_rg27.36
Total atoms total_atoms3846
Residues n_residues462
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 dmax81.1
Rg (real space) rg_real27.39
Rg uncertainty (real space) rg_real_error0.53
I(0) (real space) i0_real4.9330e+07
I(0) uncertainty (real space) i0_real_error6.7810e+05
Rg (reciprocal space) rg_reciprocal27.43
I(0) (reciprocal space) i0_reciprocal49330000.0000
Solution quality estimate total_estimate0.7447
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.4
Skewness Skewness skewness0.122
Kurtosis Kurtosis kurtosis-0.730
Angular range angular_range— – 0.2900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9162000.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.989; Stabil: 1.000; Sysdev: 0.267; Positv: 1.000; Valcen: 0.999; Smooth: 0.912

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_idd6cn5a_
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_idd6cn5b_
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_id6cn5A00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology565 — Retinoid X Receptor
Homologous superfamily homologous superfamily10 — Retinoid X Receptor
Domain ID domain_id6cn5B00
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)