3t42

Human aldose reductase in complex with a nitrile-containing IDD inhibitor

Method: X-RAY DIFFRACTION Dmax: 61.5 Å Quality: GOOD

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

Aldose reductase

Homo sapiens

UniProt P15121

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 1–316 Not recorded NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 3T4 {5-chloro-2-[(4-cyano-3-nitrobenzyl)carbamoyl]phenoxy}acetic acid × 1 CIT CITRIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 4.2;298 K;The hanging drop method was used to obtain crystals (EasyXtal Tool 24 culture plates, Qiagen). WT hALR2 was co-crystallized with the oxidized form of coenzyme NADP+ (Sigma) and inhibitor 2 at room temperature (ratios of protein / inhibitor / coenzyme = 1/2/2). Hanging drops were made by the mixing mother liquor (0.06 M citric acid, 0.04 M Bis-tris propane, 12% (w/v) PEG 3350, pH 4.2) with holoenzyme solution (10 mg/mL, 20 mM hepes, pH 7.0). Crystals were observed after three days of equilibration, EVAPORATION, temperature 298K Resolution 1.28 Å R-free 0.178

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.

169 other PDB entries and 173 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ALDR_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 4–319; UniProt 1–316

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 3t42

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3t42
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3t42
Deposition date deposition_date2011-07-25
Structure title titleHuman aldose reductase in complex with a nitrile-containing IDD inhibitor
Keywords keywordsTim Barrel, oxidoreductase-oxidoreductase inhibitor complex; oxidoreductase/oxidoreductase inhibitor
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier19.83
Radius of gyration Rg (electron density) rg_electron18.67
Forward intensity I(0) i023070200.00
Molecular weight molecular_weight37177.0 kDa
Excluded volume excluded_volume46652 ų
Envelope volume envelope_volume50872 ų
Hydration-shell volume shell_volume21968 ų
Envelope diameter envelope_diameter63.7
Shell Rg shell_rg25.82
Envelope Rg envelope_rg19.07
Shape Rg shape_rg18.66
Total Rg total_rg19.60
Total atoms total_atoms2613
Residues n_residues316
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 dmax61.5
Rg (real space) rg_real19.67
Rg uncertainty (real space) rg_real_error0.23
I(0) (real space) i0_real2.3070e+07
I(0) uncertainty (real space) i0_real_error2.4810e+05
Rg (reciprocal space) rg_reciprocal19.70
I(0) (reciprocal space) i0_reciprocal23070000.0000
Solution quality estimate total_estimate0.8986
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.1
Skewness Skewness skewness0.136
Kurtosis Kurtosis kurtosis-0.462
Angular range angular_range— – 0.4000 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha6488000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.901; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.984

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3t42a_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.7 — NAD(P)-linked oxidoreductase
Family Family familyc.1.7.1 — Aldo-keto reductases (NADP)

CATH v4.4 (1 domains)

Domain ID domain_id3t42A00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily100 — NADP-dependent oxidoreductase domain

8. Citations (1)

9. Files and Curves (10)