SAXSdb — 8c5d

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

Glutathione S-transferase P 1

Mus musculus

UniProt P19157

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	GOL GLYCEROL × 2 GTB S-(P-NITROBENZYL)GLUTATHIONE × 2 NA SODIUM ION × 11 CA CALCIUM ION × 4 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；PEG 6000 20% (w/v), 0.2 M calcium chloride dihydrate, pH 8.0	Resolution 1.28 Å R-free 0.200

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.

Other PDB	Difference from Current Entry 8C5D	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BAY GLUTATHIONE S-TRANSFERASE YFYF CYS 47-CARBOXYMETHYLATED CLASS PI, FREE ENZYME Deposited 1996-11-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–209（209 aa） Chain B 1–209（209 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.236
1GLP 1.8 ANGSTROMS MOLECULAR STRUCTURE OF MOUSE LIVER CLASS PI GLUTATHIONE S-TRANSFERASE COMPLEXED WITH S-(P-NITROBENZYL)GLUTATHIONE AND OTHER INHIBITORS Deposited 1994-03-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–209（209 aa） Chain B 1–209（209 aa）	Not recorded	GTS GLUTATHIONE SULFONIC ACID × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
1GLQ 1.8 ANGSTROMS MOLECULAR STRUCTURE OF MOUSE LIVER CLASS PI GLUTATHIONE S-TRANSFERASE COMPLEXED WITH S-(P-NITROBENZYL)GLUTATHIONE AND OTHER INHIBITORS Deposited 1994-03-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–209（209 aa） Chain B 1–209（209 aa）	Not recorded	GTB S-(P-NITROBENZYL)GLUTATHIONE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
1GSY GLUTATHIONE S-TRANSFERASE YFYF, CLASS PI, COMPLEXED WITH GLUTATHIONE Deposited 1996-10-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–209（209 aa） Chain B 1–209（209 aa）	Not recorded	GSH Glutathione × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.44 Å
1GSY GLUTATHIONE S-TRANSFERASE YFYF, CLASS PI, COMPLEXED WITH GLUTATHIONE Deposited 1996-10-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–209（209 aa） Chain B 1–209（209 aa）	Not recorded	GSH Glutathione × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.44 Å
1GTI MODIFIED GLUTATHIONE S-TRANSFERASE (PI) COMPLEXED WITH S (P-NITROBENZYL)GLUTATHIONE Deposited 1998-01-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–209（209 aa） Chain D 1–209（209 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	GTB S-(P-NITROBENZYL)GLUTATHIONE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.4；pH 6.4	Resolution 3.00 Å R-free 0.277
1GTI MODIFIED GLUTATHIONE S-TRANSFERASE (PI) COMPLEXED WITH S (P-NITROBENZYL)GLUTATHIONE Deposited 1998-01-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–209（209 aa） Chain B 1–209（209 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	GTB S-(P-NITROBENZYL)GLUTATHIONE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.4；pH 6.4	Resolution 3.00 Å R-free 0.277
1GTI MODIFIED GLUTATHIONE S-TRANSFERASE (PI) COMPLEXED WITH S (P-NITROBENZYL)GLUTATHIONE Deposited 1998-01-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 1–209（209 aa） Chain F 1–209（209 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	GTB S-(P-NITROBENZYL)GLUTATHIONE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.4；pH 6.4	Resolution 3.00 Å R-free 0.277
2GLR MOLECULAR STRUCTURE AT 1.8 ANGSTROMS OF MOUSE LIVER CLASS PI GLUTATHIONE S-TRANSFERASE COMPLEXED WITH S-(P-NITROBENZYL)GLUTATHIONE AND OTHER INHIBITORS Deposited 1994-05-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–209（209 aa） Chain B 1–209（209 aa）	Not recorded	GTX S-HEXYLGLUTATHIONE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å
2OA7 Mouse C14A Glutathione-S-Transferase Mutant in Complex with S-hexyl glutathione Deposited 2006-12-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–209（209 aa） Chain B 1–209（209 aa）	Mutation：C14A Mutation：C14A	GTX S-HEXYLGLUTATHIONE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å R-free 0.261
2OAC Mouse C14A Glutathione-S-Transferase Mutant in Complex with S-(p-nitrobenzyl) Glutathione Deposited 2006-12-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–209（209 aa） Chain B 1–209（209 aa）	Mutation：C14A Mutation：C14A	GTB S-(P-NITROBENZYL)GLUTATHIONE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å R-free 0.259
2OAD Structure of Glutathione-S-Transferase C169A Mutant Deposited 2006-12-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–209（209 aa） Chain B 1–209（209 aa）	Mutation：C169A Mutation：C169A	GTB S-(P-NITROBENZYL)GLUTATHIONE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å R-free 0.264
3O76 1.8 Angstroms molecular structure of mouse liver glutathione S-transferase mutant C47A complexed with S-(P-nitrobenzyl)glutathione Deposited 2010-07-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–210（209 aa） Chain B 2–210（209 aa）	Mutation：C47A Mutation：C47A	GTB S-(P-NITROBENZYL)GLUTATHIONE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4；293 K；20% PEG 6000, 0.1 M sodium citrate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 1.77 Å R-free 0.223

10 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GSTP1_MOUSE
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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8c5d
Deposition date deposition_date	2023-01-06
Structure title title	Glutathione transferase P1-1 from Mus musculus
Keywords keywords	multidrug resistance, pesticide, enzyme inhibition, drug design, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	22.04 Å
Radius of gyration Rg (electron density) rg_electron	20.97 Å
Forward intensity I(0) i0	37110700.00
Molecular weight molecular_weight	48476.0 kDa
Excluded volume excluded_volume	61153 Å³
Envelope volume envelope_volume	69245 Å³
Hydration-shell volume shell_volume	26415 Å³
Envelope diameter envelope_diameter	67.1 Å
Shell Rg shell_rg	28.37 Å
Envelope Rg envelope_rg	21.11 Å
Shape Rg shape_rg	20.97 Å
Total Rg total_rg	21.85 Å
Total atoms total_atoms	6764
Residues n_residues	418
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	64.9 Å
Rg (real space) rg_real	21.85 Å
Rg uncertainty (real space) rg_real_error	0.21 Å
I(0) (real space) i0_real	3.7110e+07
I(0) uncertainty (real space) i0_real_error	3.9720e+05
Rg (reciprocal space) rg_reciprocal	21.89 Å
I(0) (reciprocal space) i0_reciprocal	37110000.0000
Solution quality estimate total_estimate	0.9107
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.1 Å
Skewness Skewness skewness	0.087
Kurtosis Kurtosis kurtosis	-0.537
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8784000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.953; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.999

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Glutathione S-transferase P 1
Molecular weight formula_weight	23635.2 kDa
EC 编号 ec_number	2.5.1.18
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7434

MPPYTIVYFPVRGRCEAMRMLLADQGQSWKEEVVTIDTWMQGLLKPTCLYGQLPKFEDGDLTLYQSNAILRHLGRSLGLYGKNQREAAQMDMVNDGVEDLRGKYVTLIYTNYENGKNDYVKALPGHLKPFETLLSQNQGGKAFIVGDQISFADYNLLDLLLIHQVLAPGCLDNFPLLSAYVARLSARPKIKAFLSSPEHVNRPINGNGKQ

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	S-(P-NITROBENZYL)GLUTATHIONE
Molecular weight formula_weight	442.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	11

Entity 5 Entity 5 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	602

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8. Citations (1)

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Unit-cell length a length_a	56.617 Å
Unit-cell length b length_b	77.366 Å
Unit-cell length c length_c	101.444 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	1.280 Å
Low-resolution limit resolution_low	38.680 Å
R factor r_factor	0.1756
R_work r_work	0.1752
R_free r_free	0.1999

fit	/app/data/saxs_computation/c5/8c5d/8c5d.fit
pddf	/app/data/pr_computation/c5/8c5d/8c5d.pr.out
profile	/app/data/saxs_computation/c5/8c5d/8c5d.dat

Glutathione transferase P1-1 from Mus musculus

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

Glutathione S-transferase P 1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction