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1edu

CRYSTAL STRUCTURE OF THE ENTH DOMAIN OF RAT EPSIN 1

Method: X-RAY DIFFRACTION Dmax: 53.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

EH domain binding protein EPSIN

Rattus norvegicus

UniProt O88339

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 12–160 Fragment：N-TERMINAL FRAGMENT Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG 4000, Na-HEPES, ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 20K Resolution 1.80 Å R-free 0.224

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.

Other PDB Difference from Current Entry 1EDU Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1EYH CRYSTAL STRUCTURE OF THE EPSIN N-TERMINAL HOMOLOGY (ENTH) DOMAIN AT 1.56 ANGSTROM RESOLUTION Deposited 2000-05-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 15–158（144 aa） Fragment：ENTH DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；30% PEG 4000, 100mM Tris-HCl pH 8.5, 0.2M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Resolution 1.56 Å R-free 0.226
1H0A Epsin ENTH bound to Ins(1,4,5)P3 Deposited 2002-06-12 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–158（158 aa） Fragment：ENTH DOMAIN, RESIDUES 1-158
Not recorded DIO 1,4-DIETHYLENE DIOXIDE × 5 I3P D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；35-38% DIOXANE, pH 7.40
Resolution 1.70 Å R-free 0.228
1KY6 AP-2 CLATHRIN ADAPTOR ALPHA-APPENDAGE IN COMPLEX WITH EPSIN DPW PEPTIDE Deposited 2002-02-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain P 375–381（7 aa） Fragment：RESIDUES 375-381
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å R-free 0.245

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name EPN1_RAT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–149； UniProt 12–160

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 1edu

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1edu
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1edu
Deposition date deposition_date2000-01-28
Structure title titleCRYSTAL STRUCTURE OF THE ENTH DOMAIN OF RAT EPSIN 1
Keywords keywordsALPHA-HELIX, ENDOCYTOSIS-EXOCYTOSIS COMPLEX; ENDOCYTOSIS/EXOCYTOSIS
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier16.73 Å
Radius of gyration Rg (electron density) rg_electron15.56 Å
Forward intensity I(0) i06679370.00
Molecular weight molecular_weight17788.0 kDa
Excluded volume excluded_volume21799 ų
Envelope volume envelope_volume25582 ų
Hydration-shell volume shell_volume13891 ų
Envelope diameter envelope_diameter53.1 Å
Shell Rg shell_rg21.47 Å
Envelope Rg envelope_rg16.23 Å
Shape Rg shape_rg15.64 Å
Total Rg total_rg16.40 Å
Total atoms total_atoms1226
Residues n_residues143
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax53.9 Å
Rg (real space) rg_real16.66 Å
Rg uncertainty (real space) rg_real_error0.27 Å
I(0) (real space) i0_real6.6790e+06
I(0) uncertainty (real space) i0_real_error7.8890e+04
Rg (reciprocal space) rg_reciprocal16.67 Å
I(0) (reciprocal space) i0_reciprocal6679000.0000
Solution quality estimate total_estimate0.8946
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary52.5 Å
Skewness Skewness skewness0.206
Kurtosis Kurtosis kurtosis-0.417
Angular range angular_range— – 0.4750 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1441000.0000
Real-space data points n_real_points78
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.876; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.999
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1edua_
Class classa — All alpha proteins
Fold Fold folda.118 — alpha-alpha superhelix
Superfamily Superfamily superfamilya.118.9 — ENTH/VHS domain
Family Family familya.118.9.1 — ENTH domain

CATH v4.4 (1 domains)

Domain ID domain_id1eduA00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily90 —
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8. Citations (1)

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9. Files and Curves (10)