1c72

TYR115, GLN165 AND TRP209 CONTRIBUTE TO THE 1,2-EPOXY-3-(P-NITROPHENOXY)PROPANE CONJUGATING ACTIVITIES OF GLUTATHIONE S-TRANSFERASE CGSTM1-1

Method: X-RAY DIFFRACTION D_max: 115.0 Å Quality: REASONABLE

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

PROTEIN (GLUTATHIONE S-TRANSFERASE)

Gallus gallus

UniProt P20136

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 2–220 Chain B； UniProt 2–220	Not recorded	EPY 1-HYDROXY-2-S-GLUTATHIONYL-3-PARA-NITROPHENOXY-PROPANE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；pH 7.5	Resolution 2.80 Å R-free 0.280
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 2–220 Chain D； UniProt 2–220	Not recorded	EPY 1-HYDROXY-2-S-GLUTATHIONYL-3-PARA-NITROPHENOXY-PROPANE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；pH 7.5	Resolution 2.80 Å R-free 0.280

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 1C72	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1GSU AN AVIAN CLASS-MU GLUTATHIONE S-TRANSFERASE, CGSTM1-1 AT 1.94 ANGSTROM RESOLUTION Deposited 1997-09-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–219（219 aa） Chain B 1–219（219 aa）	Not recorded	GTX S-HEXYLGLUTATHIONE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.94 Å R-free 0.290

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GSTM2_CHICK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–219； UniProt 2–220 Author chain B； PDBConstruct 1–219； UniProt 2–220 Author chain C； PDBConstruct 1–219； UniProt 2–220 Author chain D； PDBConstruct 1–219； UniProt 2–220

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1c72
Deposition date deposition_date	2000-02-02
Structure title title	TYR115, GLN165 AND TRP209 CONTRIBUTE TO THE 1,2-EPOXY-3-(P-NITROPHENOXY)PROPANE CONJUGATING ACTIVITIES OF GLUTATHIONE S-TRANSFERASE CGSTM1-1
Keywords keywords	GLUTATHIONE S-TRANSFERASE, 1, 2-EPOXY-3-(P-NITROPHENOXY)PROPANE, EPOXIDASE ACTIVITY, STEADY-STATE KINETICS, 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	35.13 Å
Radius of gyration Rg (electron density) rg_electron	34.76 Å
Forward intensity I(0) i0	158167000.00
Molecular weight molecular_weight	103900.0 kDa
Excluded volume excluded_volume	131080 Å³
Envelope volume envelope_volume	166960 Å³
Hydration-shell volume shell_volume	41108 Å³
Envelope diameter envelope_diameter	117.9 Å
Shell Rg shell_rg	40.23 Å
Envelope Rg envelope_rg	34.32 Å
Shape Rg shape_rg	34.75 Å
Total Rg total_rg	35.17 Å
Total atoms total_atoms	7332
Residues n_residues	868
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	115.0 Å
Rg (real space) rg_real	35.31 Å
Rg uncertainty (real space) rg_real_error	0.74 Å
I(0) (real space) i0_real	1.5820e+08
I(0) uncertainty (real space) i0_real_error	2.5830e+06
Rg (reciprocal space) rg_reciprocal	35.20 Å
I(0) (reciprocal space) i0_reciprocal	158200000.0000
Solution quality estimate total_estimate	0.6586
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	33.2 Å
Skewness Skewness skewness	0.434
Kurtosis Kurtosis kurtosis	-0.587
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	75300000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.778; Stabil: 1.000; Sysdev: 0.186; Positv: 1.000; Valcen: 0.915; Smooth: 0.751

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	PROTEIN (GLUTATHIONE S-TRANSFERASE)
Molecular weight formula_weight	25779.7 kDa
EC 编号 ec_number	2.5.1.18
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	7490

VVTLGYWDIRGLAHAIRLLLEYTETPYQERRYKAGPAPDFDPSDWTNEKEKLGLDFPNLPYLIDGDVKLTQSNAILRYIARKHNMCGETEVEKQRVDVLENHLMDLRMAFARLCYSPDFEKLKPAYLELLPGKLRQLSRFLGSRSWFVGDKLTFVDFLAYDVLDQQRMFVPDCPELQGNLSQFLQRFEALEKISAYMRSGRFMKAPIFWYTALWNNKKE

来源 Source

来源生物 organism	Gallus gallus
通用名 common_name	chicken
NCBI Class编号 ncbi_taxonomy_id	9031
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	1-HYDROXY-2-S-GLUTATHIONYL-3-PARA-NITROPHENOXY-PROPANE
Molecular weight formula_weight	502.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	158

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1c72a1
Class class	a — All alpha proteins
Fold Fold fold	a.45 — GST C-terminal domain-like
Superfamily Superfamily superfamily	a.45.1 — GST C-terminal domain-like
Family Family family	a.45.1.1 — Glutathione S-transferase (GST), C-terminal domain

Domain ID domain_id	d1c72a2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.47 — Thioredoxin fold
Superfamily Superfamily superfamily	c.47.1 — Thioredoxin-like
Family Family family	c.47.1.5 — Glutathione S-transferase (GST), N-terminal domain

Domain ID domain_id	d1c72b1
Class class	a — All alpha proteins
Fold Fold fold	a.45 — GST C-terminal domain-like
Superfamily Superfamily superfamily	a.45.1 — GST C-terminal domain-like
Family Family family	a.45.1.1 — Glutathione S-transferase (GST), C-terminal domain

Domain ID domain_id	d1c72b2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.47 — Thioredoxin fold
Superfamily Superfamily superfamily	c.47.1 — Thioredoxin-like
Family Family family	c.47.1.5 — Glutathione S-transferase (GST), N-terminal domain

Domain ID domain_id	d1c72c1
Class class	a — All alpha proteins
Fold Fold fold	a.45 — GST C-terminal domain-like
Superfamily Superfamily superfamily	a.45.1 — GST C-terminal domain-like
Family Family family	a.45.1.1 — Glutathione S-transferase (GST), C-terminal domain

Domain ID domain_id	d1c72c2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.47 — Thioredoxin fold
Superfamily Superfamily superfamily	c.47.1 — Thioredoxin-like
Family Family family	c.47.1.5 — Glutathione S-transferase (GST), N-terminal domain

Domain ID domain_id	d1c72d1
Class class	a — All alpha proteins
Fold Fold fold	a.45 — GST C-terminal domain-like
Superfamily Superfamily superfamily	a.45.1 — GST C-terminal domain-like
Family Family family	a.45.1.1 — Glutathione S-transferase (GST), C-terminal domain

Domain ID domain_id	d1c72d2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.47 — Thioredoxin fold
Superfamily Superfamily superfamily	c.47.1 — Thioredoxin-like
Family Family family	c.47.1.5 — Glutathione S-transferase (GST), N-terminal domain

CATH v4.4 (8 domains)

Domain ID domain_id	1c72A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

Domain ID domain_id	1c72A02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1c72B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

Domain ID domain_id	1c72B02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1c72C01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

Domain ID domain_id	1c72C02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1c72D01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

Domain ID domain_id	1c72D02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	10 —

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8. Citations (2)

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Unit-cell length a length_a	125.600 Å
Unit-cell length b length_b	136.650 Å
Unit-cell length c length_c	125.740 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	32

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	31.000 Å
R factor r_factor	0.1900
R_work r_work	0.1900
R_free r_free	0.2800

fit	/app/data/saxs_computation/c7/1c72/1c72.fit
pddf	/app/data/pr_computation/c7/1c72/1c72.pr.out
profile	/app/data/saxs_computation/c7/1c72/1c72.dat