5dcg

Crystal Structure of WT Apo Human Glutathione Transferase Pi

Method: X-RAY DIFFRACTION Dmax: 65.5 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 1–210 Chain B; UniProt 1–210 Not recorded MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 PO4 PHOSPHATE ION × 2 CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;293 K;100MM MES, PH 6.0, 28% (W/V) PEG 8000, 20MM CACL2, 10MM DTT Resolution 2.01 Å R-free 0.190

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 1–210; UniProt 1–210 Author chain B; PDBConstruct 1–210; UniProt 1–210

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 5dcg

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5dcg
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5dcg
Deposition date deposition_date2015-08-24
Structure title titleCrystal Structure of WT Apo Human Glutathione Transferase Pi
Keywords keywordsTransferase, Anti-cancer, Apo; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier22.22
Radius of gyration Rg (electron density) rg_electron21.08
Forward intensity I(0) i035170900.00
Molecular weight molecular_weight46849.0 kDa
Excluded volume excluded_volume59097 ų
Envelope volume envelope_volume68476 ų
Hydration-shell volume shell_volume26175 ų
Envelope diameter envelope_diameter68.0
Shell Rg shell_rg28.42
Envelope Rg envelope_rg21.11
Shape Rg shape_rg21.06
Total Rg total_rg22.04
Total atoms total_atoms6587
Residues n_residues418
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 dmax65.5
Rg (real space) rg_real22.03
Rg uncertainty (real space) rg_real_error0.24
I(0) (real space) i0_real3.5170e+07
I(0) uncertainty (real space) i0_real_error4.1440e+05
Rg (reciprocal space) rg_reciprocal22.06
I(0) (reciprocal space) i0_reciprocal35170000.0000
Solution quality estimate total_estimate0.9105
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.3
Skewness Skewness skewness0.089
Kurtosis Kurtosis kurtosis-0.536
Angular range angular_range— – 0.3600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8106000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.952; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.998

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_idd5dcga1
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_idd5dcga2
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_idd5dcgb1
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_idd5dcgb2
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_id5dcgA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id5dcgA02
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_id5dcgB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id5dcgB02
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)