3kmo

Crystal Structure of the Human GST Pi C47S/Y108V Double Mutant in Complex with the Ethacrynic Acid-Glutathione Conjugate (Grown in the Absence of the Reducing Agent DTT)

Method: X-RAY DIFFRACTION Dmax: 64.8 Å Quality: EXCELLENT

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

Glutathione S-transferase P

Homo sapiens

UniProt P09211

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 2–210 Chain B; UniProt 2–210 Mutation:C47S, Y108V GSH Glutathione × 2 CA CALCIUM ION × 6 EAA ETHACRYNIC ACID × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;298 K;4mg/ml, 267mM calcium acetate, 100mM MES pH 6.0, 20% (w/v) PEG 8000 , VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.60 Å R-free 0.254

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.

67 other PDB entries and 77 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GSTP1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–209; UniProt 2–210 Author chain B; PDBConstruct 1–209; UniProt 2–210

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 3kmo

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3kmo
Deposition date deposition_date2009-11-11
Structure title titleCrystal Structure of the Human GST Pi C47S/Y108V Double Mutant in Complex with the Ethacrynic Acid-Glutathione Conjugate (Grown in the Absence of the Reducing Agent DTT)
Keywords keywordsTRANSFERASE, GLUTATHIONE, DETOXIFICATION, DOUBLE MUTANT, ETHACRYNIC ACID, DIURETIC DRUG, DIMER INTERFACE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier21.98
Radius of gyration Rg (electron density) rg_electron20.92
Forward intensity I(0) i036028200.00
Molecular weight molecular_weight47647.0 kDa
Excluded volume excluded_volume60167 ų
Envelope volume envelope_volume69058 ų
Hydration-shell volume shell_volume26465 ų
Envelope diameter envelope_diameter66.2
Shell Rg shell_rg28.35
Envelope Rg envelope_rg21.01
Shape Rg shape_rg20.90
Total Rg total_rg21.89
Total atoms total_atoms3343
Residues n_residues417
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 dmax64.8
Rg (real space) rg_real21.79
Rg uncertainty (real space) rg_real_error0.22
I(0) (real space) i0_real3.6030e+07
I(0) uncertainty (real space) i0_real_error4.8400e+05
Rg (reciprocal space) rg_reciprocal21.83
I(0) (reciprocal space) i0_reciprocal36030000.0000
Solution quality estimate total_estimate0.9081
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.0
Skewness Skewness skewness0.090
Kurtosis Kurtosis kurtosis-0.520
Angular range angular_range— – 0.3600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10460000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.946; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.988

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd3kmoa1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.47 — Thioredoxin fold
Superfamily Superfamily superfamilyc.47.1 — Thioredoxin-like
Family Family familyc.47.1.0 — automated matches
Domain ID domain_idd3kmoa2
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_idd3kmob1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.47 — Thioredoxin fold
Superfamily Superfamily superfamilyc.47.1 — Thioredoxin-like
Family Family familyc.47.1.0 — automated matches
Domain ID domain_idd3kmob2
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 (4 domains)

Domain ID domain_id3kmoA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id3kmoA02
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_id3kmoB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id3kmoB02
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)