PDB-9nxu: Crystal Structure of Glutathione S-Transferase Per a 5 (delta class)

ID or keywords:

Entry

Database: PDB / ID: 9nxu

Title

Crystal Structure of Glutathione S-Transferase Per a 5 (delta class)

Components

Glutathione S transferase class delta

Keywords

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

Function / homology

Function and homology information

glutathione transferase activity / glutathione metabolic process
Similarity search - Function

Biological species

Periplaneta americana (American cockroach)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.3 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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PDBx/mmCIF format	9nxu.cif.gz	272.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9nxu.ent.gz	223.1 KB	Display	PDB format
PDBx/mmJSON format	9nxu.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/9nxu ftp://data.pdbj.org/pub/pdb/validation_reports/nx/9nxu	HTTPS FTP

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Related structure data

Related structure data	9nxtC 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 (9)

Deposited unit

A: Glutathione S transferase class delta

B: Glutathione S transferase class delta

hetero molecules

51 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	51.678, 57.549, 72.497
Angle α, β, γ (deg.)	90.00, 92.75, 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, 2 molecules AB

#1: Protein	Glutathione S transferase class delta Mass: 24753.541 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Periplaneta americana (American cockroach) Production host: Escherichia coli (E. coli) / References: UniProt: A0A2K9YV03

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Non-polymers , 5 types, 457 molecules

#2: Chemical	ChemComp-GSH / Glutathione Type: peptide-like, Peptide-like / Class: Oxidation-reduction / Mass: 307.323 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₃O₆S Source: (gene. exp.) Periplaneta americana (American cockroach) Production host: Escherichia coli (E. coli) / Feature type: SUBJECT OF INVESTIGATION / References: BIRD: PRD_002593
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 445 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.15 Å³/Da / Density % sol: 42.75 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1M Tris pH 8.5, 0.2M MgCl2, 28% PEG4000

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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 9M / Detector: PIXEL / Date: Feb 9, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.3→33.45 Å / Num. obs: 103391 / % possible obs: 99.06 % / Redundancy: 2 % / B_iso Wilson estimate: 17.81 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.019 / Net I/σ(I): 16.5
Reflection shell	Resolution: 1.3→1.35 Å / Num. unique obs: 10165 / CC_1/2: 0.816

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Processing

Software

Name	Version	Classification
PHENIX	(1.21.1_5286: ???)	refinement
autoPROC		data reduction
autoPROC		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.3→30.34 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.83 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1609	1562	1.51 %
R_work	0.1508	-	-
obs	0.1509	103377	99.04 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.3→30.34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3422	0	43	445	3910

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	3666
X-RAY DIFFRACTION	f_angle_d	0.877	4978
X-RAY DIFFRACTION	f_dihedral_angle_d	14.241	1367
X-RAY DIFFRACTION	f_chiral_restr	0.066	534
X-RAY DIFFRACTION	f_plane_restr	0.007	652

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 (%)
1.3-1.34	0.2843	136	0.2485	9103	X-RAY DIFFRACTION	98
1.34-1.39	0.2503	147	0.2258	9121	X-RAY DIFFRACTION	98
1.39-1.45	0.243	132	0.2048	9157	X-RAY DIFFRACTION	98
1.45-1.51	0.2325	145	0.1853	9180	X-RAY DIFFRACTION	99
1.51-1.59	0.1733	131	0.1637	9183	X-RAY DIFFRACTION	99
1.59-1.69	0.1795	150	0.155	9253	X-RAY DIFFRACTION	99
1.69-1.82	0.2002	145	0.1582	9271	X-RAY DIFFRACTION	99
1.82-2	0.1649	145	0.1517	9329	X-RAY DIFFRACTION	100
2-2.29	0.1418	144	0.1437	9343	X-RAY DIFFRACTION	100
2.29-2.89	0.16	145	0.144	9412	X-RAY DIFFRACTION	100
2.89-30.34	0.1388	142	0.1393	9463	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	4.9236	-0.012	0.4998	2.1139	-0.7474	1.2197	0.032	-0.2588	-0.1206	0.182	0.0098	0.2019	0.0382	-0.1244	-0.0448	0.1542	-0.0046	0.0292	0.1604	0.0047	0.1771	9.1549	0.5018	33.4847
2	4.0593	-0.4363	0.4212	2.2503	-0.8389	2.5862	-0.0134	0.1104	-0.3382	0.0316	0.1053	0.4901	0.0494	-0.4918	-0.0875	0.1651	-0.0129	0.0369	0.2622	0.0007	0.2869	-1.3783	2.7523	30.2001
3	1.8999	0.2218	0.1193	1.6765	0.0929	1.539	0.0349	-0.2111	0.126	0.1079	-0.0068	0.1236	-0.1092	-0.0698	-0.0267	0.1711	0.006	0.0297	0.1939	-0.0174	0.1735	8.7603	11.0617	32.9926
4	1.539	0.7322	1.1254	3.3818	1.0404	2.8849	0.0499	0.0279	-0.0849	-0.1855	-0.0069	0.1423	0.12	-0.0529	-0.0249	0.1318	0.0218	0.005	0.1624	-0.0011	0.1633	16.314	2.8049	19.3381
5	6.4967	1.9444	3.7212	3.3945	1.0967	4.8468	0.1573	0.7703	-0.3012	-0.4695	-0.0294	-0.0113	0.2689	0.5414	-0.1399	0.2508	0.0819	0.0171	0.2723	-0.0329	0.1672	22.5913	-3.3598	10.5029
6	2.2815	-0.3228	0.6355	2.5475	0.6989	2.3693	0.0889	0.0677	-0.0845	-0.0465	-0.0527	-0.1638	0.1798	0.234	-0.0455	0.1487	0.0321	0.0145	0.177	0.0022	0.1622	24.8577	-3.9309	23.7717
7	6.5989	2.6122	4.8979	3.0621	3.717	7.2083	0.1056	-0.0015	-0.49	-0.0025	-0.1275	0.19	0.3665	-0.3041	0.0037	0.2089	-0.0079	-0.0033	0.1632	-0.014	0.2859	10.22	-12.5028	26.9745
8	2.7101	-0.9274	-0.3418	2.4323	0.459	2.4593	-0.017	0.2646	0.189	-0.3375	-0.0815	-0.2327	-0.1614	0.3345	0.1	0.2155	-0.0195	0.0094	0.2301	0.0532	0.1868	20.3593	23.9121	9.1186
9	2.2272	-1.3298	-1.3952	6.5946	4.1783	5.1715	-0.1048	0.4218	0.0291	-0.5675	-0.0099	-0.0976	0.1389	0.2607	0.1281	0.4348	-0.0537	0.0433	0.4328	0.0825	0.2663	25.7213	21.3489	3.5316
10	1.9646	0.267	-0.3688	1.8213	-0.616	2.3892	-0.0938	0.2477	-0.0945	-0.4294	-0.0934	-0.4126	0.1152	0.4467	0.1252	0.1991	-0.0014	0.0689	0.2551	0.0482	0.2221	26.557	16.1729	12.9833
11	5.8641	1.7414	-2.2386	5.0051	-1.3305	4.8048	0.0937	-0.2132	0.5227	0.5622	-0.2833	0.0487	-0.8638	0.2088	0.1668	0.3161	-0.0399	-0.0483	0.2051	-0.0393	0.2313	15.1939	26.6666	27.5959
12	0.954	0.6641	1.8487	0.7601	1.4139	5.0449	0.0119	0.0708	-0.0737	-0.0905	0.0543	0.0365	0.0369	0.0452	-0.0811	0.1933	0.0052	-0.0189	0.1516	-0.0082	0.1853	7.0292	11.7945	10.9012
13	1.2542	0.6397	0.3921	3.9829	3.8625	7.8074	0.0778	0.0685	-0.1548	0.0024	-0.0125	0.1598	0.3639	-0.244	-0.0395	0.1691	-0.0134	-0.0402	0.1484	0.011	0.1931	-3.0828	11.3169	11.4355
14	6.5812	1.9588	2.161	3.9825	1.6975	2.8583	-0.0764	-0.6432	0.4817	0.3958	-0.0512	0.5154	-0.1314	-0.3424	0.0996	0.2433	0.0467	0.0277	0.2378	-0.0168	0.2391	1.6976	25.5807	22.9837
15	1.5769	0.4806	0.4069	1.4149	-0.0054	1.3362	-0.0646	0.0851	0.053	-0.139	0.0324	0.1359	-0.1333	-0.0609	0.0409	0.1967	0.0038	-0.0243	0.1538	0.0032	0.1675	1.7793	23.6559	10.108
16	3.5224	0.3309	-0.1018	5.855	3.6193	7.5365	-0.115	0.4573	-0.1247	-0.5524	-0.0342	-0.0986	0.0024	0.1152	0.1162	0.2733	-0.0129	-0.0053	0.2407	0.0328	0.1871	11.0016	23.6551	-1.2236

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 24 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 25 through 55 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 56 through 78 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 79 through 125 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 126 through 142 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 143 through 191 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 192 through 216 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 2 through 24 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 25 through 38 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 39 through 78 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 79 through 88 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 89 through 125 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 126 through 142 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 143 through 155 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 156 through 191 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 192 through 216 )

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