3e7c

Glucocorticoid Receptor LBD bound to GSK866

Method: X-RAY DIFFRACTION Dmax: 82.9 Å Quality: EXCELLENT

1. Protein Identity and Related Structures Protein Identity & Related Structures

Glucocorticoid receptor

Homo sapiens

UniProt P04150

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 521–777 Chain B; UniProt 521–777 Fragment:UNP RESIDUES 521-777 Mutation:F602Y, C638G Nuclear receptor coactivator 2 × 2 (Q15596) 866 5-amino-N-[(2S)-2-({[(2,6-dichlorophenyl)carbonyl](ethyl)amino}methyl)-3,3,3-trifluoro-2-hydroxypropyl]-1-(4-fluorophenyl)-1H-pyrazole-4-carboxamide × 2 GOL GLYCEROL × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;295 K;0.1M MES pH 6.5, 1.6M MgSO4, 0.1% betahexaglucoside, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.15 Å R-free 0.266
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 521–777 Fragment:UNP RESIDUES 521-777 Mutation:F602Y, C638G Nuclear receptor coactivator 2 × 1 (Q15596) 866 5-amino-N-[(2S)-2-({[(2,6-dichlorophenyl)carbonyl](ethyl)amino}methyl)-3,3,3-trifluoro-2-hydroxypropyl]-1-(4-fluorophenyl)-1H-pyrazole-4-carboxamide × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;295 K;0.1M MES pH 6.5, 1.6M MgSO4, 0.1% betahexaglucoside, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.15 Å R-free 0.266
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 521–777 Fragment:UNP RESIDUES 521-777 Mutation:F602Y, C638G Nuclear receptor coactivator 2 × 1 (Q15596) 866 5-amino-N-[(2S)-2-({[(2,6-dichlorophenyl)carbonyl](ethyl)amino}methyl)-3,3,3-trifluoro-2-hydroxypropyl]-1-(4-fluorophenyl)-1H-pyrazole-4-carboxamide × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;295 K;0.1M MES pH 6.5, 1.6M MgSO4, 0.1% betahexaglucoside, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.15 Å R-free 0.266

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.

54 other PDB entries and 77 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GCR_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 5–257; UniProt 521–777 Author chain B; PDBConstruct 3–257; UniProt 521–777

Nuclear receptor coactivator 2

OrganismNot specified

UniProt Q15596

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain D; UniProt 741–751 Chain H; UniProt 741–751 Fragment:UNP RESIDUES 741-751 Glucocorticoid receptor × 2 (P04150) 866 5-amino-N-[(2S)-2-({[(2,6-dichlorophenyl)carbonyl](ethyl)amino}methyl)-3,3,3-trifluoro-2-hydroxypropyl]-1-(4-fluorophenyl)-1H-pyrazole-4-carboxamide × 2 GOL GLYCEROL × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;295 K;0.1M MES pH 6.5, 1.6M MgSO4, 0.1% betahexaglucoside, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.15 Å R-free 0.266
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain H; UniProt 741–751 Fragment:UNP RESIDUES 741-751 Glucocorticoid receptor × 1 (P04150) 866 5-amino-N-[(2S)-2-({[(2,6-dichlorophenyl)carbonyl](ethyl)amino}methyl)-3,3,3-trifluoro-2-hydroxypropyl]-1-(4-fluorophenyl)-1H-pyrazole-4-carboxamide × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;295 K;0.1M MES pH 6.5, 1.6M MgSO4, 0.1% betahexaglucoside, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.15 Å R-free 0.266
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 741–751 Fragment:UNP RESIDUES 741-751 Glucocorticoid receptor × 1 (P04150) 866 5-amino-N-[(2S)-2-({[(2,6-dichlorophenyl)carbonyl](ethyl)amino}methyl)-3,3,3-trifluoro-2-hydroxypropyl]-1-(4-fluorophenyl)-1H-pyrazole-4-carboxamide × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;295 K;0.1M MES pH 6.5, 1.6M MgSO4, 0.1% betahexaglucoside, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.15 Å R-free 0.266

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.

283 other PDB entries and 332 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NCOA2_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain D; PDBConstruct 1–11; UniProt 741–751 Author chain H; PDBConstruct 1–11; UniProt 741–751

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 3e7c

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3e7c
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3e7c
Deposition date deposition_date2008-08-18
Structure title titleGlucocorticoid Receptor LBD bound to GSK866
Keywords keywords;GR, Glucocorticoid Receptor, Nuclear Receptor, Alternative initiation, Chromatin regulator, Disease mutation, DNA-binding, Lipid-binding, Metal-binding, Nucleus, Phosphoprotein, Pseudohermaphroditism, Receptor, Steroid-binding, Transcription, Transcription regulation, Zinc-finger, Activator ;; TRANSCRIPTION
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier27.42
Radius of gyration Rg (electron density) rg_electron26.19
Forward intensity I(0) i054633500.00
Molecular weight molecular_weight60400.0 kDa
Excluded volume excluded_volume76726 ų
Envelope volume envelope_volume91856 ų
Hydration-shell volume shell_volume28853 ų
Envelope diameter envelope_diameter83.3
Shell Rg shell_rg33.99
Envelope Rg envelope_rg25.97
Shape Rg shape_rg26.20
Total Rg total_rg27.03
Total atoms total_atoms4237
Residues n_residues514
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 dmax82.9
Rg (real space) rg_real27.33
Rg uncertainty (real space) rg_real_error0.44
I(0) (real space) i0_real5.4630e+07
I(0) uncertainty (real space) i0_real_error7.8460e+05
Rg (reciprocal space) rg_reciprocal27.36
I(0) (reciprocal space) i0_reciprocal54630000.0000
Solution quality estimate total_estimate0.9145
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary30.0
Skewness Skewness skewness0.149
Kurtosis Kurtosis kurtosis-0.737
Angular range angular_range— – 0.2900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15540000.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.976; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.958

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3e7ca_
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.123.1.1 — Nuclear receptor ligand-binding domain
Domain ID domain_idd3e7cb_
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.123.1.1 — Nuclear receptor ligand-binding domain

CATH v4.4 (2 domains)

Domain ID domain_id3e7cA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology565 — Retinoid X Receptor
Homologous superfamily homologous superfamily10 — Retinoid X Receptor
Domain ID domain_id3e7cB00
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)