1ydk

Crystal structure of the I219A mutant of human glutathione transferase A1-1 with S-hexylglutathione

Method: X-RAY DIFFRACTION Dmax: 66.2 Å Quality: EXCELLENT

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

Glutathione S-transferase A1

Homo sapiens

UniProt P08263

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 1–221 Chain B; UniProt 1–221 Mutation:I219A GTX S-HEXYLGLUTATHIONE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;PEG 2000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.95 Å R-free 0.253

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.

38 other PDB entries and 57 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GSTA1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–222; UniProt 1–221 Author chain B; PDBConstruct 2–222; UniProt 1–221

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 1ydk

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1ydk
Deposition date deposition_date2004-12-24
Structure title titleCrystal structure of the I219A mutant of human glutathione transferase A1-1 with S-hexylglutathione
Keywords keywordsGlutathione transferase, S-hexylglutathione, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier22.60
Radius of gyration Rg (electron density) rg_electron21.37
Forward intensity I(0) i036797800.00
Molecular weight molecular_weight49828.0 kDa
Excluded volume excluded_volume63743 ų
Envelope volume envelope_volume74125 ų
Hydration-shell volume shell_volume27739 ų
Envelope diameter envelope_diameter67.3
Shell Rg shell_rg29.09
Envelope Rg envelope_rg21.42
Shape Rg shape_rg21.37
Total Rg total_rg22.32
Total atoms total_atoms3505
Residues n_residues426
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 dmax66.2
Rg (real space) rg_real22.42
Rg uncertainty (real space) rg_real_error0.22
I(0) (real space) i0_real3.6800e+07
I(0) uncertainty (real space) i0_real_error3.6780e+05
Rg (reciprocal space) rg_reciprocal22.47
I(0) (reciprocal space) i0_reciprocal36800000.0000
Solution quality estimate total_estimate0.9093
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.1
Skewness Skewness skewness0.059
Kurtosis Kurtosis kurtosis-0.544
Angular range angular_range— – 0.3500 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9178000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.954; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.979

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1ydka1
Class classa — All alpha proteins
Fold Fold folda.45 — GST C-terminal domain-like
Superfamily Superfamily superfamilya.45.1 — GST C-terminal domain-like
Family Family familya.45.1.1 — Glutathione S-transferase (GST), C-terminal domain
Domain ID domain_idd1ydka2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.47 — Thioredoxin fold
Superfamily Superfamily superfamilyc.47.1 — Thioredoxin-like
Family Family familyc.47.1.5 — Glutathione S-transferase (GST), N-terminal domain
Domain ID domain_idd1ydkb1
Class classa — All alpha proteins
Fold Fold folda.45 — GST C-terminal domain-like
Superfamily Superfamily superfamilya.45.1 — GST C-terminal domain-like
Family Family familya.45.1.1 — Glutathione S-transferase (GST), C-terminal domain
Domain ID domain_idd1ydkb2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.47 — Thioredoxin fold
Superfamily Superfamily superfamilyc.47.1 — Thioredoxin-like
Family Family familyc.47.1.5 — Glutathione S-transferase (GST), N-terminal domain

CATH v4.4 (4 domains)

Domain ID domain_id1ydkA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id1ydkA02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily10
Domain ID domain_id1ydkB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id1ydkB02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily10

8. Citations (1)

9. Files and Curves (10)