4zjr

RORgamma in complex with inverse agonist 48

Method: X-RAY DIFFRACTION Dmax: 115.6 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 265–487 Fragment:ligand binding domain (UNP Residues 265-487) 4P3 6-chloro-4'-[(2-chloro-6-fluorobenzoyl)(methyl)amino]-3'-(2,2,2-trifluoroethoxy)biphenyl-3-carboxamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;298 K;1.0M Sodium Acetate, 0.2M Sodium Chloride, 0.1M TRIS pH 8.0 Resolution 2.70 Å R-free 0.223
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 265–487 Fragment:ligand binding domain (UNP Residues 265-487) 4P3 6-chloro-4'-[(2-chloro-6-fluorobenzoyl)(methyl)amino]-3'-(2,2,2-trifluoroethoxy)biphenyl-3-carboxamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;298 K;1.0M Sodium Acetate, 0.2M Sodium Chloride, 0.1M TRIS pH 8.0 Resolution 2.70 Å R-free 0.223
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 265–487 Fragment:ligand binding domain (UNP Residues 265-487) 4P3 6-chloro-4'-[(2-chloro-6-fluorobenzoyl)(methyl)amino]-3'-(2,2,2-trifluoroethoxy)biphenyl-3-carboxamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;298 K;1.0M Sodium Acetate, 0.2M Sodium Chloride, 0.1M TRIS pH 8.0 Resolution 2.70 Å R-free 0.223
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 265–487 Fragment:ligand binding domain (UNP Residues 265-487) 4P3 6-chloro-4'-[(2-chloro-6-fluorobenzoyl)(methyl)amino]-3'-(2,2,2-trifluoroethoxy)biphenyl-3-carboxamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;298 K;1.0M Sodium Acetate, 0.2M Sodium Chloride, 0.1M TRIS pH 8.0 Resolution 2.70 Å R-free 0.223

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 264 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 3–225; UniProt 265–487 Author chain B; PDBConstruct 3–225; UniProt 265–487 Author chain C; PDBConstruct 3–225; UniProt 265–487 Author chain D; PDBConstruct 3–225; UniProt 265–487

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 4zjr

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4zjr
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4zjr
Deposition date deposition_date2015-04-29
Structure title titleRORgamma in complex with inverse agonist 48
Keywords keywordsRORgamma ligand binding domain, Inverse agonist, TRANSCRIPTION; TRANSCRIPTION
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier34.09
Radius of gyration Rg (electron density) rg_electron33.41
Forward intensity I(0) i0169293000.00
Molecular weight molecular_weight102520.0 kDa
Excluded volume excluded_volume127710 ų
Envelope volume envelope_volume172580 ų
Hydration-shell volume shell_volume42883 ų
Envelope diameter envelope_diameter121.1
Shell Rg shell_rg40.36
Envelope Rg envelope_rg32.55
Shape Rg shape_rg33.42
Total Rg total_rg33.96
Total atoms total_atoms7185
Residues n_residues876
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 dmax115.6
Rg (real space) rg_real34.01
Rg uncertainty (real space) rg_real_error1.19
I(0) (real space) i0_real1.6930e+08
I(0) uncertainty (real space) i0_real_error2.7140e+06
Rg (reciprocal space) rg_reciprocal34.06
I(0) (reciprocal space) i0_reciprocal169300000.0000
Solution quality estimate total_estimate0.8642
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary45.2
Skewness Skewness skewness0.265
Kurtosis Kurtosis kurtosis-0.178
Angular range angular_range— – 0.2300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha47920000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.768; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.931

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd4zjra_
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_idd4zjrb_
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_idd4zjrc1
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_idd4zjrc2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4zjrd1
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_idd4zjrd2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id4zjrA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology565 — Retinoid X Receptor
Homologous superfamily homologous superfamily10 — Retinoid X Receptor
Domain ID domain_id4zjrB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology565 — Retinoid X Receptor
Homologous superfamily homologous superfamily10 — Retinoid X Receptor
Domain ID domain_id4zjrC00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology565 — Retinoid X Receptor
Homologous superfamily homologous superfamily10 — Retinoid X Receptor
Domain ID domain_id4zjrD00
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)