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9yxy

Crystal structure of EEPD1 EEP domain dimer at pH 5.5

Method: X-RAY DIFFRACTION Dmax: 96.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Endonuclease/exonuclease/phosphatase family domain-containing protein 1

Homo sapiens

UniProt Q7L9B9

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 245–543 Chain B； UniProt 245–543 Not recorded GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 1 IMD IMIDAZOLE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；288 K；0.1 M Bis-Tris, pH 5.5, 25% PEG3350 Resolution 2.00 Å R-free 0.232

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 9YXY Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9YI2 Human EEPD1 EEP domain dimer Deposited 2025-10-01 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–569（568 aa）
Chain B 2–569（568 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
9YSF Crystal structure of EEPD1 EEP domain dimer with Mg(II) Deposited 2025-10-17 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 254–543（290 aa）
Not recorded EDO 1,2-ETHANEDIOL × 8 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 MG MAGNESIUM ION × 4 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；288 K；0.1 M Tris, pH 8.5, 0.3 M magnesium chloride, 25% w/v PEG3350
Resolution 1.59 Å R-free 0.204

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name EEPD1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–302； UniProt 245–543 Author chain B； PDBConstruct 4–302； UniProt 245–543

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 9yxy

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9yxy
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9yxy
Deposition date deposition_date2025-10-27
Structure title titleCrystal structure of EEPD1 EEP domain dimer at pH 5.5
Keywords keywordsEndonuclease/Exonuclease/Phosphatase Fold, Dimerization, Replication stress response, DNA BINDING PROTEIN; DNA BINDING PROTEIN
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_guinier29.57 Å
Radius of gyration Rg (electron density) rg_electron29.25 Å
Forward intensity I(0) i054391100.00
Molecular weight molecular_weight58275.0 kDa
Excluded volume excluded_volume73091 ų
Envelope volume envelope_volume90620 ų
Hydration-shell volume shell_volume26678 ų
Envelope diameter envelope_diameter98.1 Å
Shell Rg shell_rg35.45 Å
Envelope Rg envelope_rg29.04 Å
Shape Rg shape_rg29.23 Å
Total Rg total_rg29.93 Å
Total atoms total_atoms8186
Residues n_residues526
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 dmax96.8 Å
Rg (real space) rg_real29.75 Å
Rg uncertainty (real space) rg_real_error0.75 Å
I(0) (real space) i0_real5.4390e+07
I(0) uncertainty (real space) i0_real_error7.9990e+05
Rg (reciprocal space) rg_reciprocal29.68 Å
I(0) (reciprocal space) i0_reciprocal54390000.0000
Solution quality estimate total_estimate0.8369
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.9 Å
Skewness Skewness skewness0.428
Kurtosis Kurtosis kurtosis-0.613
Angular range angular_range— – 0.2700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha16020000.0000
Real-space data points n_real_points55
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.730; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.863; Smooth: 0.824
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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8. Citations (1)

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9. Files and Curves (10)