8vkz

Crystal structure of Glucocorticoid Receptor in complex with an inhibitor

Method: X-RAY DIFFRACTION Dmax: 101.4 Å Quality: GOOD

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 528–777 Chain B; UniProt 528–777 Mutation:V571M, F602S, C638D Nuclear receptor coactivator 2 × 2 (Q15596) A1ACE (4aR,4bS,5R,6aS,6bS,8R,9aR,10aR,10bR)-8-{4-[(3-aminophenyl)methyl]phenyl}-5-hydroxy-6b-(hydroxyacetyl)-4a,6a-dimethyl-4a,4b,5,6,6a,6b,9a,10,10a,10b,11,12-dodecahydro-2H,8H-naphtho[2',1':4,5]indeno[1,2-d][1,3]dioxol-2-one × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 5.5;296 K;24% (w/v) PEG 400, 200 mM ammonium acetate, 100 mM sodium citrate pH 5.5 Resolution 2.13 Å R-free 0.245

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 79 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 3–252; UniProt 528–777 Author chain B; PDBConstruct 3–252; UniProt 528–777

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 740–753 Chain E; UniProt 740–753 Not recorded Glucocorticoid receptor × 2 (P04150) A1ACE (4aR,4bS,5R,6aS,6bS,8R,9aR,10aR,10bR)-8-{4-[(3-aminophenyl)methyl]phenyl}-5-hydroxy-6b-(hydroxyacetyl)-4a,6a-dimethyl-4a,4b,5,6,6a,6b,9a,10,10a,10b,11,12-dodecahydro-2H,8H-naphtho[2',1':4,5]indeno[1,2-d][1,3]dioxol-2-one × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 5.5;296 K;24% (w/v) PEG 400, 200 mM ammonium acetate, 100 mM sodium citrate pH 5.5 Resolution 2.13 Å R-free 0.245

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 334 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 1–14; UniProt 740–753 Author chain E; PDBConstruct 1–14; UniProt 740–753

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 8vkz

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id8vkz
Deposition date deposition_date2024-01-10
Structure title titleCrystal structure of Glucocorticoid Receptor in complex with an inhibitor
Keywords keywordsGlucocorticord Receptor, modulator, TRANSCRIPTION, TRANSCRIPTION-INHIBITOR complex; TRANSCRIPTION/INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier28.17
Radius of gyration Rg (electron density) rg_electron27.67
Forward intensity I(0) i051125200.00
Molecular weight molecular_weight59034.0 kDa
Excluded volume excluded_volume75143 ų
Envelope volume envelope_volume90462 ų
Hydration-shell volume shell_volume28077 ų
Envelope diameter envelope_diameter106.2
Shell Rg shell_rg33.93
Envelope Rg envelope_rg27.95
Shape Rg shape_rg27.69
Total Rg total_rg28.23
Total atoms total_atoms4147
Residues n_residues497
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 dmax101.4
Rg (real space) rg_real28.38
Rg uncertainty (real space) rg_real_error0.88
I(0) (real space) i0_real5.1130e+07
I(0) uncertainty (real space) i0_real_error7.8530e+05
Rg (reciprocal space) rg_reciprocal28.32
I(0) (reciprocal space) i0_reciprocal51120000.0000
Solution quality estimate total_estimate0.8156
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.2
Skewness Skewness skewness0.504
Kurtosis Kurtosis kurtosis-0.305
Angular range angular_range— – 0.2800 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha20560000.0000
Real-space data points n_real_points57
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.642; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.718; Smooth: 0.955

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (1)

9. Files and Curves (10)