3i6a

Human GST A1-1 GIMF mutant with Glutathione

Method: X-RAY DIFFRACTION Dmax: 180.6 Å Quality: GOOD

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 1–222 Chain B; UniProt 1–222 Mutation:A12G, L107I, L108M, V111F, M208P, K211I, S212Y, L213V, E214R, E215T, A216V, R217Y, K218N, F222P GSH Glutathione × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;293 K;18% PEG 4000, 0.1 M Tric-Cl, 10 mM DTT, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 1.98 Å R-free 0.244
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 1–222 Chain D; UniProt 1–222 Mutation:A12G, L107I, L108M, V111F, M208P, K211I, S212Y, L213V, E214R, E215T, A216V, R217Y, K218N, F222P GSH Glutathione × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;293 K;18% PEG 4000, 0.1 M Tric-Cl, 10 mM DTT, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 1.98 Å R-free 0.244
3 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain E; UniProt 1–222 Chain F; UniProt 1–222 Mutation:A12G, L107I, L108M, V111F, M208P, K211I, S212Y, L213V, E214R, E215T, A216V, R217Y, K218N, F222P GSH Glutathione × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;293 K;18% PEG 4000, 0.1 M Tric-Cl, 10 mM DTT, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 1.98 Å R-free 0.244
4 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain G; UniProt 1–222 Chain H; UniProt 1–222 Mutation:A12G, L107I, L108M, V111F, M208P, K211I, S212Y, L213V, E214R, E215T, A216V, R217Y, K218N, F222P GSH Glutathione × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;293 K;18% PEG 4000, 0.1 M Tric-Cl, 10 mM DTT, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 1.98 Å R-free 0.244

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 54 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 1–222; UniProt 1–222 Author chain B; PDBConstruct 1–222; UniProt 1–222 Author chain C; PDBConstruct 1–222; UniProt 1–222 Author chain D; PDBConstruct 1–222; UniProt 1–222 Author chain E; PDBConstruct 1–222; UniProt 1–222 Author chain F; PDBConstruct 1–222; UniProt 1–222 Author chain G; PDBConstruct 1–222; UniProt 1–222 Author chain H; PDBConstruct 1–222; UniProt 1–222

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 3i6a

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3i6a
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3i6a
Deposition date deposition_date2009-07-06
Structure title titleHuman GST A1-1 GIMF mutant with Glutathione
Keywords keywordshuman GST A1-1, enzyme, Transferase; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier54.37
Radius of gyration Rg (electron density) rg_electron55.17
Forward intensity I(0) i0536451000.00
Molecular weight molecular_weight204660.0 kDa
Excluded volume excluded_volume261520 ų
Envelope volume envelope_volume368620 ų
Hydration-shell volume shell_volume61422 ų
Envelope diameter envelope_diameter193.2
Shell Rg shell_rg50.06
Envelope Rg envelope_rg54.14
Shape Rg shape_rg55.17
Total Rg total_rg54.97
Total atoms total_atoms14412
Residues n_residues1752
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 dmax180.6
Rg (real space) rg_real55.01
Rg uncertainty (real space) rg_real_error2.74
I(0) (real space) i0_real5.3650e+08
I(0) uncertainty (real space) i0_real_error1.2930e+07
Rg (reciprocal space) rg_reciprocal53.82
I(0) (reciprocal space) i0_reciprocal535500000.0000
Solution quality estimate total_estimate0.7541
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary37.4
Skewness Skewness skewness0.571
Kurtosis Kurtosis kurtosis-0.396
Angular range angular_range— – 0.1450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha48010000.0000
Real-space data points n_real_points30
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.694; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.705; Smooth: 0.012

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

Domain ID domain_idd3i6aa1
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_idd3i6aa2
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_idd3i6ab1
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_idd3i6ab2
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_idd3i6ac1
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_idd3i6ac2
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_idd3i6ad1
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_idd3i6ad2
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_idd3i6ae1
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_idd3i6ae2
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_idd3i6af1
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_idd3i6af2
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_idd3i6ag1
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_idd3i6ag2
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_idd3i6ah1
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_idd3i6ah2
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

CATH v4.4 (16 domains)

Domain ID domain_id3i6aA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id3i6aA02
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_id3i6aB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id3i6aB02
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_id3i6aC01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id3i6aC02
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_id3i6aD01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id3i6aD02
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_id3i6aE01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id3i6aE02
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_id3i6aF01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id3i6aF02
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_id3i6aG01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id3i6aG02
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_id3i6aH01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id3i6aH02
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)