PDB-9nxt: Crystal Structure of Glutathione S-Transferase Per a 23 (sigma class)

ID or keywords:

Entry

Database: PDB / ID: 9nxt

Title

Crystal Structure of Glutathione S-Transferase Per a 23 (sigma class)

Components

glutathione transferase

Keywords

TRANSFERASE / Glutathione S-Transferase / GST / GSH / American cockroach / allergen

Function / homology

Function and homology information

glutathione peroxidase activity / glutathione transferase / glutathione transferase activity / glutathione metabolic process
Similarity search - Function

Biological species

Periplaneta americana (American cockroach)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

Zong, G. / Pedersen, L.C. / Mueller, G.A.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	1ZIAES102906	United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	1ZICES102645	United States

Citation

Journal: Clin Exp Allergy / Year: 2026
Title: Reclassification of GST Allergens Based on Their Cross-Reactivity in Two Divergent Cockroach Species.
Authors: Zong, G. / Lozano, A. / Leighton, G.O. / Randall, T. / Pedersen, L.C. / Glesner, J. / Smith, B.R.E. / Acevedo, N. / Schal, C. / Caraballo, L. / Pomes, A. / Zakzuk, J. / Mueller, G.A.

History

Deposition	Mar 26, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 22, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9nxt.cif.gz	494.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9nxt.ent.gz	414.8 KB	Display	PDB format
PDBx/mmJSON format	9nxt.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nx/9nxt ftp://data.pdbj.org/pub/pdb/validation_reports/nx/9nxt	HTTPS FTP

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Related structure data

Related structure data	9nxuC 9nxvC 9nxwC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#212 - Aug 2017 Glutathione Transferases similarity (10) #255 - Mar 2021 Cisplatin and DNA similarity (10)

Deposited unit

A: glutathione transferase

B: glutathione transferase

C: glutathione transferase

D: glutathione transferase

hetero molecules

98.3 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: glutathione transferase

B: glutathione transferase

hetero molecules

defined by author&software
Evidence: gel filtration
49.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: glutathione transferase

D: glutathione transferase

hetero molecules

defined by author&software
49.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	98.729, 49.619, 103.440
Angle α, β, γ (deg.)	90.00, 118.10, 90.00
Int Tables number	4
Space group name H-M	P12₁1
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

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Protein , 1 types, 4 molecules ABCD

#1: Protein	glutathione transferase Mass: 23723.217 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Periplaneta americana (American cockroach) Production host: Escherichia coli (E. coli) / References: UniProt: A0A2P0XJ18, glutathione transferase

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Non-polymers , 6 types, 720 molecules

#2: Chemical	ChemComp-GDS / OXIDIZED GLUTATHIONE DISULFIDE Mass: 612.631 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₀H₃₂N₆O₁₂S₂
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₆O₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#6: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 702 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.3 Å³/Da / Density % sol: 46.5 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 18mM MgCl2, 18mM CaCl2, 0.1M HEPES/MOPS, pH7.5, 9.375% MPD, 9.375% PEG1000, 9.375%PEG3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 24, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.5→49.39 Å / Num. obs: 277798 / % possible obs: 99.8 % / Redundancy: 1.96 % / B_iso Wilson estimate: 19.2 Å² / CC_1/2: 0.996 / Net I/σ(I): 8.8
Reflection shell	Resolution: 1.5→1.55 Å / Num. unique obs: 26835 / CC_1/2: 0.705

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Processing

Software

Name	Version	Classification
PHENIX	(1.21.2_5419: ???)	refinement
autoPROC		data reduction
autoPROC		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.5→35.88 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.04 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1938	1542	1.09 %
R_work	0.1702	-	-
obs	0.1705	141492	99.77 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.5→35.88 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6481	0	169	702	7352

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	6956
X-RAY DIFFRACTION	f_angle_d	0.875	9426
X-RAY DIFFRACTION	f_dihedral_angle_d	13.359	2568
X-RAY DIFFRACTION	f_chiral_restr	0.055	960
X-RAY DIFFRACTION	f_plane_restr	0.009	1206

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.5-1.55	0.2584	146	0.2641	12644	X-RAY DIFFRACTION	100
1.55-1.6	0.2361	136	0.2283	12668	X-RAY DIFFRACTION	100
1.6-1.67	0.2199	140	0.2063	12667	X-RAY DIFFRACTION	100
1.67-1.74	0.2083	151	0.1943	12609	X-RAY DIFFRACTION	100
1.74-1.84	0.2225	137	0.1892	12716	X-RAY DIFFRACTION	100
1.84-1.95	0.2167	135	0.1852	12671	X-RAY DIFFRACTION	100
1.95-2.1	0.2034	129	0.1698	12696	X-RAY DIFFRACTION	100
2.1-2.31	0.1769	145	0.1639	12710	X-RAY DIFFRACTION	100
2.31-2.65	0.1725	142	0.1649	12740	X-RAY DIFFRACTION	100
2.65-3.34	0.2021	135	0.169	12813	X-RAY DIFFRACTION	100
3.34-35.88	0.1796	146	0.1524	13016	X-RAY DIFFRACTION	99

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	4.365	1.2064	-1.7062	3.8459	-0.9878	4.1096	-0.097	0.0996	-0.3138	-0.088	0.0879	-0.0645	0.3977	0.0907	-0.021	0.1372	0.0118	-0.021	0.0963	-0.0389	0.106	14.533	-10.8987	5.5971
2	2.2209	2.9555	-0.3318	6.1646	-1.1605	3.8206	-0.0622	0.2004	-0.2231	-0.1126	0.2173	0.044	0.642	-0.3961	-0.1908	0.2652	-0.0334	0.0121	0.1175	0.0055	0.1897	5.7941	-15.5589	18.0757
3	1.6415	-0.4354	0.1162	0.7964	-0.0573	1.4408	-0.0321	-0.0071	0.0018	-0.0104	0.0578	0.078	-0.0172	0.0393	-0.0299	0.1135	-0.0005	-0.0129	0.0795	-0.0074	0.1247	11.8638	5.0013	11.0214
4	3.5852	-1.1225	-2.5328	1.1137	-0.0055	2.8733	0.0175	0.4368	0.0278	-0.0974	-0.0347	0.1822	-0.2709	-0.2411	0.015	0.1914	-0.0168	-0.0517	0.2079	0.0068	0.1848	7.9045	8.8046	-1.3933
5	7.8507	5.0256	-4.2183	5.2731	-2.1131	4.0889	-0.2529	0.4701	0.0384	-0.1899	0.1292	0.1774	0.1904	-0.3416	0.1441	0.1413	-0.0215	-0.0409	0.1873	-0.0348	0.1442	11.0125	-6.0779	-3.9214
6	6.1805	-1.334	1.869	5.1585	-0.8801	3.3604	-0.1169	-0.0302	0.4091	0.2133	0.0765	-0.1812	-0.42	0.2252	0.0239	0.2407	-0.0333	-0.0228	0.1389	-0.0389	0.1272	20.645	15.3319	32.4432
7	5.71	-2.5515	0.1692	1.7885	0.0171	0.0193	-0.0674	-0.3469	0.3647	0.1518	0.1725	-0.0264	-0.6601	-0.0579	-0.0693	0.3354	0.0204	-0.0161	0.077	-0.0038	0.2032	10.0493	21.7585	23.613
8	2.3518	2.4168	0.9468	2.5052	0.728	4.9909	-0.2421	0.0877	0.5261	-0.0997	0.118	-0.0778	-0.8373	0.5423	0.0852	0.2818	-0.0608	-0.031	0.1696	-0.0033	0.2808	22.2837	17.7288	21.5308
9	4.5856	-1.5001	0.0008	4.9782	0.5805	3.6016	-0.1051	-0.0922	-0.0716	0.0219	0.1438	-0.2098	-0.0217	0.5088	-0.0298	0.1039	-0.0046	-0.0085	0.1806	-0.0116	0.0981	27.2524	4.0697	24.0613
10	6.8894	-2.3985	-4.9939	3.0013	1.6396	5.8982	0.0259	0.0944	-0.0334	0.1114	-0.0377	0.149	0.0506	-0.033	0.0403	0.1626	-0.003	-0.0076	0.0854	-0.0008	0.1438	13.6379	-2.3909	25.1202
11	8.1546	1.0642	0.3867	5.2416	-2.6652	4.66	0.0503	-0.2448	0.1346	0.3631	0.0475	1.2802	-0.1971	-0.9551	-0.0998	0.2707	0.006	0.0752	0.4083	-0.0721	0.3501	-5.686	0.7849	31.9966
12	3.0212	-1.3787	3.7997	1.2837	-2.3116	5.4078	0.1851	0.0989	-0.6101	0.0111	-0.0919	-0.1026	0.6426	0.0406	-0.1272	0.2897	-0.0039	0.0326	0.0949	-0.0115	0.2162	12.293	-11.2913	32.574
13	1.9113	-0.0115	0.4356	2.4244	-0.7665	2.4309	0.0084	-0.2379	-0.1324	0.3605	-0.0303	0.0768	0.1345	-0.0307	0.0226	0.2232	0.0034	0.002	0.1225	-0.0028	0.1337	16.0596	-1.9564	36.96
14	3.1127	-1.3701	2.6219	4.3698	0.3822	3.0945	-0.2363	-0.8677	0.2218	0.5741	0.1318	-0.1136	-0.1349	-0.237	0.096	0.2951	-0.0031	-0.0212	0.2636	-0.0396	0.1485	20.5603	10.25	42.909
15	1.6667	-0.6286	-1.4207	0.2287	0.5616	1.2779	-0.5448	-0.875	-0.7749	0.1485	-0.1448	-0.5378	0.9497	1.4925	-0.1782	0.2216	0.4105	0.0609	0.9969	0.3127	0.3604	47.5006	-4.5795	-10.02
16	4.3526	1.4956	-0.3172	2.589	0.5253	1.7446	-0.2541	-0.1308	0.1139	-0.1234	0.1777	-0.0492	0.0593	0.3105	0.0765	0.1379	-0.0153	0.0061	0.2589	-0.0055	0.0978	34.8033	5.3243	-16.3739
17	2.2194	1.0538	-1.5177	0.6828	-0.7635	1.0419	0.1469	-0.0141	0.2896	0.1637	-0.109	-0.3311	-0.0922	0.4287	-0.031	0.2609	-0.2017	0.0569	0.605	-0.0994	0.4261	54.0487	21.5239	-20.7305
18	7.5549	6.4899	-7.1851	5.8657	-5.4738	8.5814	0.3358	0.0199	0.8188	0.1087	0.1523	0.2782	-0.6586	0.1498	-0.4778	0.2311	-0.0956	0.0233	0.2319	-0.0356	0.2664	34.0171	20.4443	-14.7931
19	1.3149	0.2637	-0.0112	0.2778	0.019	0.0579	0.0847	-0.5794	0.2506	0.1235	0.0654	-0.1045	-0.3319	0.859	-0.0944	0.2	-0.163	0.0039	0.5523	-0.0921	0.2117	37.8264	13.2908	-6.984
20	0.1903	0.0663	-0.2639	0.2914	-0.5413	1.1674	0.0051	-0.2668	-0.01	-0.0056	-0.2951	-0.4222	-0.1541	0.8941	-0.0106	0.2385	-0.0555	-0.1358	1.4195	0.1612	0.0973	44.6296	4.5344	2.0556
21	3.0269	0.1445	0.221	5.9128	0.5967	3.5907	-0.1414	0.2967	0.0408	-0.3298	0.018	0.3708	0.046	-0.3946	0.1021	0.217	-0.0566	-0.0424	0.3202	0.0074	0.1464	27.0449	7.4461	-37.0376
22	4.9828	1.7047	-3.5393	5.8327	-1.6145	8.1098	0.1173	0.3675	0.538	-0.4469	0.1871	0.3532	-1.1554	-0.0861	-0.2351	0.3359	-0.046	-0.0419	0.2089	0.0538	0.2457	31.0484	20.7094	-30.5911
23	7.5786	-1.0063	-0.0767	6.5888	1.4323	6.264	-0.0631	0.2324	0.1298	-0.1764	0.0412	0.7383	-0.3854	-0.8327	0.0242	0.1655	-0.0034	-0.0244	0.2725	0.0537	0.2387	23.6054	11.1483	-26.9279
24	4.6247	0.455	-0.0509	4.698	0.0949	3.9828	-0.3357	0.1201	-0.2663	-0.0782	0.0927	0.1712	0.5816	-0.3292	0.2247	0.2228	-0.0767	0.0491	0.2323	-0.0234	0.1534	27.1986	-2.9171	-25.7056
25	8.5203	5.2343	-4.3203	8.1526	-3.7023	6.3439	-0.3086	-0.2356	-0.3512	-0.0932	0.0641	-0.225	0.3677	0.5108	0.267	0.1947	0.0515	0.0412	0.258	-0.0063	0.1288	42.1792	-0.7573	-26.5391
26	3.8735	-0.9261	-1.0755	4.4701	0.2001	2.6187	-0.0948	0.0754	0.4865	-0.1184	0.1034	-1.1902	-0.3654	0.9331	0.0055	0.3115	-0.1259	0.0422	0.582	-0.0371	0.4272	56.7942	10.6168	-35.4901
27	6.717	3.8005	0.0698	8.4192	1.041	3.5387	-0.3882	-0.091	-0.704	-0.063	0.2131	-0.4126	0.7833	0.8321	0.1764	0.3243	0.1463	0.1128	0.4039	0.0314	0.2856	48.9826	-8.057	-31.5801
28	3.1521	-0.099	-0.6546	2.3261	-0.1239	3.1573	-0.2555	0.2845	-0.3697	-0.2173	0.0792	-0.1015	0.5736	0.2654	0.1603	0.3436	-0.0196	0.0784	0.3043	-0.05	0.2232	40.3486	-5.2428	-37.9977
29	4.0862	1.2041	1.8906	2.0407	-0.2626	5.6897	-0.1873	0.5795	0.1483	-0.5576	0.0121	-0.1897	0.0818	0.2257	0.1587	0.3668	-0.0822	-0.0105	0.4347	-0.0113	0.2239	31.0151	2.0239	-45.6123

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 36 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 37 through 53 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 54 through 167 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 168 through 189 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 190 through 205 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 3 through 36 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 37 through 53 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 54 through 64 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 65 through 82 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 83 through 107 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 108 through 125 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 126 through 140 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 141 through 188 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 189 through 205 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 3 through 64 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 65 through 107 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 108 through 125 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 126 through 140 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 141 through 189 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 190 through 205 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 3 through 36 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 37 through 53 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 54 through 64 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 65 through 82 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 83 through 107 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 108 through 125 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 126 through 140 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 141 through 189 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 190 through 205 )

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Protein , 1 types, 4 molecules ABCD

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Non-polymers , 6 types, 720 molecules

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-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 4 molecules ABCD

-
Non-polymers , 6 types, 720 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi