PDB-9vp5: Glucose-6-phosphate dehydrogenase from Leishmania donovani

ID or keywords:

Entry

Database: PDB / ID: 9vp5

Title

Glucose-6-phosphate dehydrogenase from Leishmania donovani

Components

Glucose-6-phosphate 1-dehydrogenase

Keywords

OXIDOREDUCTASE / Glucose-6-phosphate dehydrogenase / Rossmann fold / apo form

Function / homology

Function and homology information

glucose-6-phosphate dehydrogenase (NADP+) / glucose-6-phosphate dehydrogenase activity / pentose-phosphate shunt, oxidative branch / glucose metabolic process / NADP binding
Similarity search - Function

Biological species

Leishmania donovani (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Jakkula, P. / Qureshi, I.A.

Funding support

India, 1items

Citation

Journal: Int.J.Biol.Macromol. / Year: 2025
Title: Crystal structure of leishmanial glucose-6-phosphate dehydrogenase and its implications for selective inhibitor development.
Authors: Jakkula, P. / Qureshi, I.A.

History

Deposition	Jul 2, 2025	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 5, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9vp5.cif.gz	229.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9vp5.ent.gz	172.7 KB	Display	PDB format
PDBx/mmJSON format	9vp5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9vp5_validation.pdf.gz	461.2 KB	Display	wwPDB validaton report
Full document	9vp5_full_validation.pdf.gz	469.4 KB	Display
Data in XML	9vp5_validation.xml.gz	46.4 KB	Display
Data in CIF	9vp5_validation.cif.gz	63.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vp/9vp5 ftp://data.pdbj.org/pub/pdb/validation_reports/vp/9vp5	HTTPS FTP

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Related structure data

Related structure data	9vp6C 9vp7C 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

Deposited unit

A: Glucose-6-phosphate 1-dehydrogenase

B: Glucose-6-phosphate 1-dehydrogenase

hetero molecules

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

1

A: Glucose-6-phosphate 1-dehydrogenase

B: Glucose-6-phosphate 1-dehydrogenase

hetero molecules

A: Glucose-6-phosphate 1-dehydrogenase

B: Glucose-6-phosphate 1-dehydrogenase

hetero molecules

defined by author&software
Evidence: gel filtration
268 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	191.327, 97.356, 70.346
Angle α, β, γ (deg.)	90.000, 93.829, 90.000
Int Tables number	5
Space group name H-M	C121

#1: Protein	Glucose-6-phosphate 1-dehydrogenase Mass: 66933.812 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania donovani (eukaryote) Gene: g6pdh, CGC20_2515, CGC21_25385, LDBPK_340080, LdCL_340005900, LDHU3_34.0110 Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A2CIK6, glucose-6-phosphate dehydrogenase (NADP+)
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 2.45 Å³/Da / Density % sol: 52.3 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 4% Tacsimate, 12% PEG3350, 4-8% Glycerol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.968 Å
Detector	Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 11, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.968 Å / Relative weight: 1
Reflection	Resolution: 2.4→54.886 Å / Num. obs: 49811 / % possible obs: 98.9 % / Redundancy: 4.8 % / CC_1/2: 0.978 / Net I/σ(I): 6.8
Reflection shell	Resolution: 2.4→9.6 Å / Redundancy: 4.9 % / Num. unique obs: 4586 / CC_1/2: 0.826

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0415	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.4→54.886 Å / Cor.coef. F_o:F_c: 0.947 / Cor.coef. F_o:F_c free: 0.907 / SU B: 9.365 / SU ML: 0.213 / Cross valid method: FREE R-VALUE / ESU R: 0.377 / ESU R Free: 0.268
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2593	2525	5.07 %
R_work	0.1967	47278	-
all	0.2	-	-
obs	-	49803	98.774 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 40.975 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.255 Å²	0 Å²	-3.233 Å²
2-	-	2.106 Å²	-0 Å²
3-	-	-	0.576 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→54.886 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8026	0	4	364	8394

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.012	8189
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	7587
X-RAY DIFFRACTION	r_angle_refined_deg	1.247	1.652	11109
X-RAY DIFFRACTION	r_angle_other_deg	0.435	1.571	17409
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.092	5	1043
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.971	5	48
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.836	10	1254
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.055	10	361
X-RAY DIFFRACTION	r_chiral_restr	0.058	0.2	1255
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	9704
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1864
X-RAY DIFFRACTION	r_nbd_refined	0.216	0.2	1680
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.207	0.2	7140
X-RAY DIFFRACTION	r_nbtor_refined	0.179	0.2	4021
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	4375
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.172	0.2	315
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.005	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.197	0.2	27
X-RAY DIFFRACTION	r_nbd_other	0.232	0.2	153
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.283	0.2	12
X-RAY DIFFRACTION	r_mcbond_it	3.185	4.521	4202
X-RAY DIFFRACTION	r_mcbond_other	3.179	4.521	4202
X-RAY DIFFRACTION	r_mcangle_it	4.926	8.1	5235
X-RAY DIFFRACTION	r_mcangle_other	4.926	8.101	5236
X-RAY DIFFRACTION	r_scbond_it	3.387	4.612	3987
X-RAY DIFFRACTION	r_scbond_other	3.387	4.612	3988
X-RAY DIFFRACTION	r_scangle_it	5.347	8.41	5874
X-RAY DIFFRACTION	r_scangle_other	5.346	8.41	5875
X-RAY DIFFRACTION	r_lrange_it	7.288	43.389	8976
X-RAY DIFFRACTION	r_lrange_other	7.277	43.437	8925

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.4-2.462	0.341	211	0.262	3444	0.267	3662	0.93	0.957	99.8088	0.252
2.462-2.53	0.356	180	0.269	3430	0.273	3615	0.928	0.954	99.8617	0.256
2.53-2.603	0.312	171	0.244	3367	0.248	3542	0.939	0.962	99.8871	0.23
2.603-2.683	0.296	151	0.222	3257	0.225	3418	0.942	0.97	99.7074	0.208
2.683-2.77	0.297	144	0.212	3129	0.216	3299	0.947	0.973	99.2119	0.196
2.77-2.867	0.28	149	0.206	3002	0.209	3201	0.949	0.973	98.438	0.191
2.867-2.975	0.262	165	0.191	2877	0.195	3084	0.954	0.976	98.6381	0.179
2.975-3.096	0.27	163	0.198	2762	0.202	2981	0.954	0.975	98.1214	0.19
3.096-3.234	0.262	136	0.201	2622	0.204	2879	0.958	0.975	95.7971	0.194
3.234-3.391	0.261	109	0.201	2368	0.204	2708	0.961	0.978	91.4697	0.196
3.391-3.574	0.254	112	0.211	2455	0.212	2624	0.958	0.978	97.8277	0.208
3.574-3.789	0.238	128	0.194	2324	0.197	2452	0.968	0.983	100	0.192
3.789-4.05	0.249	111	0.177	2205	0.18	2316	0.961	0.983	100	0.178
4.05-4.372	0.223	110	0.151	2043	0.154	2153	0.967	0.986	100	0.159
4.372-4.786	0.208	116	0.144	1890	0.148	2006	0.976	0.987	100	0.154
4.786-5.346	0.216	114	0.173	1711	0.176	1825	0.971	0.984	100	0.185
5.346-6.163	0.265	74	0.2	1502	0.203	1577	0.964	0.981	99.9366	0.211
6.163-7.525	0.323	75	0.209	1299	0.214	1374	0.951	0.978	100	0.225
7.525-10.543	0.206	63	0.184	1007	0.185	1070	0.974	0.981	100	0.209
10.543-54.886	0.315	43	0.268	584	0.271	630	0.942	0.945	99.5238	0.287

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