5kra

Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with DDT and DDE

Method: X-RAY DIFFRACTION Dmax: 115.8 Å Quality: GOOD

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

Estrogen receptor

Homo sapiens

UniProt P03372

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 125–381 Chain B; UniProt 125–381 Fragment:ligand-binding domain Mutation:Y537S NCOA2 × 2 6WS 1-[2,2-bis(chloranyl)-1-(4-chlorophenyl)ethenyl]-4-chloranyl-benzene × 1 6WT 1-chloranyl-4-[2,2,2-tris(chloranyl)-1-(4-chlorophenyl)ethyl]benzene × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.3;294 K;15% PEG 3350, 0.05M MgCl2, 0.067M NaCl, 0.1M Tris Resolution 2.40 Å R-free 0.248
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain E; UniProt 125–381 Chain F; UniProt 125–381 Fragment:ligand-binding domain Mutation:Y537S NCOA2 × 2 6WS 1-[2,2-bis(chloranyl)-1-(4-chlorophenyl)ethenyl]-4-chloranyl-benzene × 1 6WT 1-chloranyl-4-[2,2,2-tris(chloranyl)-1-(4-chlorophenyl)ethyl]benzene × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.3;294 K;15% PEG 3350, 0.05M MgCl2, 0.067M NaCl, 0.1M Tris Resolution 2.40 Å R-free 0.248

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.

434 other PDB entries and 521 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ESR1_HUMAN
Isoform P03372-3
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–257; UniProt 125–381 Author chain B; PDBConstruct 1–257; UniProt 125–381 Author chain E; PDBConstruct 1–257; UniProt 125–381 Author chain F; PDBConstruct 1–257; UniProt 125–381

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 5kra

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5kra
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5kra
Deposition date deposition_date2016-07-07
Structure title titleCrystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with DDT and DDE
Keywords keywordsNuclear receptor, transcription factor, ligand binding, protein-ligand complex, TRANSCRIPTION; TRANSCRIPTION
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier35.36
Radius of gyration Rg (electron density) rg_electron34.85
Forward intensity I(0) i0177378000.00
Molecular weight molecular_weight109660.0 kDa
Excluded volume excluded_volume138370 ų
Envelope volume envelope_volume173130 ų
Hydration-shell volume shell_volume41556 ų
Envelope diameter envelope_diameter124.5
Shell Rg shell_rg40.94
Envelope Rg envelope_rg34.72
Shape Rg shape_rg34.86
Total Rg total_rg35.25
Total atoms total_atoms7650
Residues n_residues970
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 dmax115.8
Rg (real space) rg_real35.46
Rg uncertainty (real space) rg_real_error0.96
I(0) (real space) i0_real1.7740e+08
I(0) uncertainty (real space) i0_real_error2.9450e+06
Rg (reciprocal space) rg_reciprocal35.40
I(0) (reciprocal space) i0_reciprocal177400000.0000
Solution quality estimate total_estimate0.8718
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary33.4
Skewness Skewness skewness0.366
Kurtosis Kurtosis kurtosis-0.595
Angular range angular_range— – 0.2250 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha71110000.0000
Real-space data points n_real_points46
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.840; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.944; Smooth: 0.865

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id5kraA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology565 — Retinoid X Receptor
Homologous superfamily homologous superfamily10 — Retinoid X Receptor
Domain ID domain_id5kraB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology565 — Retinoid X Receptor
Homologous superfamily homologous superfamily10 — Retinoid X Receptor
Domain ID domain_id5kraE00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology565 — Retinoid X Receptor
Homologous superfamily homologous superfamily10 — Retinoid X Receptor
Domain ID domain_id5kraF00
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)