3k23

Glucocorticoid Receptor with Bound D-prolinamide 11

Method: X-RAY DIFFRACTION Dmax: 105.6 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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 521–777 Fragment:UNP residues 521-777, Ligand Binding Domain Mutation:F602Y, C638G Nuclear receptor coactivator 2 × 1 (Q15596) JZN 1-{[3-(4-{[(2R)-4-(5-fluoro-2-methoxyphenyl)-2-hydroxy-4-methyl-2-(trifluoromethyl)pentyl]amino}-6-methyl-1H-indazol-1-yl)phenyl]carbonyl}-D-prolinamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;298 K;0.1M MES 6.5, 28% PEG 5K MME, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 3.00 Å R-free 0.289
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 521–777 Fragment:UNP residues 521-777, Ligand Binding Domain Mutation:F602Y, C638G Nuclear receptor coactivator 2 × 1 (Q15596) JZN 1-{[3-(4-{[(2R)-4-(5-fluoro-2-methoxyphenyl)-2-hydroxy-4-methyl-2-(trifluoromethyl)pentyl]amino}-6-methyl-1H-indazol-1-yl)phenyl]carbonyl}-D-prolinamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;298 K;0.1M MES 6.5, 28% PEG 5K MME, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 3.00 Å R-free 0.289
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 521–777 Fragment:UNP residues 521-777, Ligand Binding Domain Mutation:F602Y, C638G Nuclear receptor coactivator 2 × 1 (Q15596) JZN 1-{[3-(4-{[(2R)-4-(5-fluoro-2-methoxyphenyl)-2-hydroxy-4-methyl-2-(trifluoromethyl)pentyl]amino}-6-methyl-1H-indazol-1-yl)phenyl]carbonyl}-D-prolinamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;298 K;0.1M MES 6.5, 28% PEG 5K MME, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 3.00 Å R-free 0.289

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 3–259; UniProt 521–777 Author chain B; PDBConstruct 3–259; UniProt 521–777 Author chain C; PDBConstruct 3–259; 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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 740–751 Fragment:UNP residues 740-751 Glucocorticoid receptor × 1 (P04150) JZN 1-{[3-(4-{[(2R)-4-(5-fluoro-2-methoxyphenyl)-2-hydroxy-4-methyl-2-(trifluoromethyl)pentyl]amino}-6-methyl-1H-indazol-1-yl)phenyl]carbonyl}-D-prolinamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;298 K;0.1M MES 6.5, 28% PEG 5K MME, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 3.00 Å R-free 0.289
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain E; UniProt 740–751 Fragment:UNP residues 740-751 Glucocorticoid receptor × 1 (P04150) JZN 1-{[3-(4-{[(2R)-4-(5-fluoro-2-methoxyphenyl)-2-hydroxy-4-methyl-2-(trifluoromethyl)pentyl]amino}-6-methyl-1H-indazol-1-yl)phenyl]carbonyl}-D-prolinamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;298 K;0.1M MES 6.5, 28% PEG 5K MME, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 3.00 Å R-free 0.289
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain F; UniProt 740–751 Fragment:UNP residues 740-751 Glucocorticoid receptor × 1 (P04150) JZN 1-{[3-(4-{[(2R)-4-(5-fluoro-2-methoxyphenyl)-2-hydroxy-4-methyl-2-(trifluoromethyl)pentyl]amino}-6-methyl-1H-indazol-1-yl)phenyl]carbonyl}-D-prolinamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;298 K;0.1M MES 6.5, 28% PEG 5K MME, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 3.00 Å R-free 0.289

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 1–12; UniProt 740–751 Author chain E; PDBConstruct 1–12; UniProt 740–751 Author chain F; PDBConstruct 1–12; UniProt 740–751

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 3k23

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3k23
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3k23
Deposition date deposition_date2009-09-29
Structure title titleGlucocorticoid Receptor with Bound D-prolinamide 11
Keywords keywords;Glucocorticoid Receptor, Steroid Hormone Receptor, Nuclear Receptor, GR, glucocorticoids, alpha helical sandwich, meta-channel, Alternative initiation, Chromatin regulator, Disease mutation, DNA-binding, Metal-binding, Nucleus, 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_guinier32.25
Radius of gyration Rg (electron density) rg_electron31.89
Forward intensity I(0) i0106426000.00
Molecular weight molecular_weight86841.0 kDa
Excluded volume excluded_volume110550 ų
Envelope volume envelope_volume139470 ų
Hydration-shell volume shell_volume37246 ų
Envelope diameter envelope_diameter114.4
Shell Rg shell_rg38.06
Envelope Rg envelope_rg31.84
Shape Rg shape_rg31.89
Total Rg total_rg32.42
Total atoms total_atoms6111
Residues n_residues767
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 dmax105.6
Rg (real space) rg_real32.35
Rg uncertainty (real space) rg_real_error0.93
I(0) (real space) i0_real1.0640e+08
I(0) uncertainty (real space) i0_real_error1.8470e+06
Rg (reciprocal space) rg_reciprocal32.31
I(0) (reciprocal space) i0_reciprocal106400000.0000
Solution quality estimate total_estimate0.8855
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary32.3
Skewness Skewness skewness0.389
Kurtosis Kurtosis kurtosis-0.438
Angular range angular_range— – 0.2450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha32560000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.895; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.966; Smooth: 0.857

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd3k23a_
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_idd3k23b_
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_idd3k23c_
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 (3 domains)

Domain ID domain_id3k23A00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology565 — Retinoid X Receptor
Homologous superfamily homologous superfamily10 — Retinoid X Receptor
Domain ID domain_id3k23B00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology565 — Retinoid X Receptor
Homologous superfamily homologous superfamily10 — Retinoid X Receptor
Domain ID domain_id3k23C00
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)