9keg

human glyoxalase I (with C-ter His tag) in complex with licochalcone B, form 2

Method: X-RAY DIFFRACTION Dmax: 67.2 Å Quality: REASONABLE

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 A1L5R 1-(4-hydroxyphenyl)-3-[2-methoxy-3,4-bis(oxidanyl)phenyl]prop-2-en-1-one × 2 PG4 TETRAETHYLENE GLYCOL × 2 BME BETA-MERCAPTOETHANOL × 3 ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.8;293 K;0.2 M Sodium chloride, 0.1 M MES, 25%(w/v) PEG 3350 Resolution 1.80 Å R-free 0.239

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 20 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

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 9keg

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9keg
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 licochalcone B, form 2
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_guinier20.62
Radius of gyration Rg (electron density) rg_electron19.62
Forward intensity I(0) i053240400.00
Molecular weight molecular_weight38303.0 kDa
Excluded volume excluded_volume37174 ų
Envelope volume envelope_volume58428 ų
Hydration-shell volume shell_volume23894 ų
Envelope diameter envelope_diameter62.0
Shell Rg shell_rg27.00
Envelope Rg envelope_rg19.93
Shape Rg shape_rg19.59
Total Rg total_rg20.36
Total atoms total_atoms2880
Residues n_residues352
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 dmax67.2
Rg (real space) rg_real20.46
Rg uncertainty (real space) rg_real_error0.25
I(0) (real space) i0_real5.3240e+07
I(0) uncertainty (real space) i0_real_error6.4040e+05
Rg (reciprocal space) rg_reciprocal20.49
I(0) (reciprocal space) i0_reciprocal53240000.0000
Solution quality estimate total_estimate0.6636
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.3
Skewness Skewness skewness0.090
Kurtosis Kurtosis kurtosis-0.508
Angular range angular_range— – 0.3850 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha13400000.0000
Real-space data points n_real_points70
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.823; Stabil: 1.000; Sysdev: 0.387; Positv: 1.000; Valcen: 0.991; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)