9kek

human glyoxalase I (with C-ter His tag) in complex with piceatannol

Method: X-RAY DIFFRACTION Dmax: 101.5 Å Quality: GOOD

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

Lactoylglutathione lyase

Homo sapiens

UniProt Q04760

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 1–184 Chain B; UniProt 1–184 Not recorded ZN ZINC ION × 2 PIT PICEATANNOL × 2 PG4 TETRAETHYLENE GLYCOL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.5;293 K;0.2 M Sodium chloride, 0.1 M Bis-Tris, 25%(w/v) PEG 3350 Resolution 2.11 Å R-free 0.233
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 1–184 Chain D; UniProt 1–184 Not recorded ZN ZINC ION × 2 PIT PICEATANNOL × 1 PG4 TETRAETHYLENE GLYCOL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.5;293 K;0.2 M Sodium chloride, 0.1 M Bis-Tris, 25%(w/v) PEG 3350 Resolution 2.11 Å R-free 0.233

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.

15 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LGUL_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–184; UniProt 1–184 Author chain B; PDBConstruct 1–184; UniProt 1–184 Author chain C; PDBConstruct 1–184; UniProt 1–184 Author chain D; PDBConstruct 1–184; UniProt 1–184

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 9kek

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9kek
Deposition date deposition_date2024-11-05
最后修订 last_revision2025-11-12
Structure title titlehuman glyoxalase I (with C-ter His tag) in complex with piceatannol
Keywords keywordsglyoxalase i, zinc metalloenzyme, lyase; LYASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier31.74
Radius of gyration Rg (electron density) rg_electron31.06
Forward intensity I(0) i0104779000.00
Molecular weight molecular_weight81958.0 kDa
Excluded volume excluded_volume102740 ų
Envelope volume envelope_volume127890 ų
Hydration-shell volume shell_volume34579 ų
Envelope diameter envelope_diameter108.0
Shell Rg shell_rg37.82
Envelope Rg envelope_rg30.81
Shape Rg shape_rg31.07
Total Rg total_rg31.65
Total atoms total_atoms11400
Residues n_residues708
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 dmax101.5
Rg (real space) rg_real31.83
Rg uncertainty (real space) rg_real_error0.75
I(0) (real space) i0_real1.0480e+08
I(0) uncertainty (real space) i0_real_error1.7010e+06
Rg (reciprocal space) rg_reciprocal31.80
I(0) (reciprocal space) i0_reciprocal104800000.0000
Solution quality estimate total_estimate0.8831
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary30.4
Skewness Skewness skewness0.343
Kurtosis Kurtosis kurtosis-0.633
Angular range angular_range— – 0.2500 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha24780000.0000
Real-space data points n_real_points51
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.882; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.966; Smooth: 0.864

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (1)

9. Files and Curves (10)