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- PDB-9vp7: Glucose-6-phosphate dehydrogenase from Leishmania donovani in com... -

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Basic information

Entry
Database: PDB / ID: 9vp7
TitleGlucose-6-phosphate dehydrogenase from Leishmania donovani in complex with pseudo substrate
ComponentsGlucose-6-phosphate 1-dehydrogenase
KeywordsOXIDOREDUCTASE / Glucose-6-phosphate dehydrogenase / Rosman fold / Complex form / pseudo substrate
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
Glucose-6-phosphate dehydrogenase, active site / Glucose-6-phosphate dehydrogenase active site. / Glucose-6-phosphate dehydrogenase / Glucose-6-phosphate dehydrogenase, NAD-binding / Glucose-6-phosphate dehydrogenase, C-terminal / Glucose-6-phosphate dehydrogenase, NAD binding domain / Glucose-6-phosphate dehydrogenase, C-terminal domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-GLP / DI(HYDROXYETHYL)ETHER / Glucose-6-phosphate 1-dehydrogenase
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsJakkula, P. / Qureshi, I.A.
Funding support India, 1items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB) India
CitationJournal: 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
DepositionJul 2, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucose-6-phosphate 1-dehydrogenase
B: Glucose-6-phosphate 1-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,04614
Polymers133,8682
Non-polymers1,17812
Water13,043724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)191.840, 97.685, 70.449
Angle α, β, γ (deg.)90.000, 94.005, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#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+)
#4: Sugar ChemComp-GLP / 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucopyranose / GLUCOSAMINE 6-PHOSPHATE / 6-O-phosphono-alpha-D-glucosamine / 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucose / 2-amino-2-deoxy-6-O-phosphono-D-glucose / 2-amino-2-deoxy-6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 259.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14NO8P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-GlcpN6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 735 molecules

#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 724 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 53.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 4% Tacsimate, 12% PEG3350, 4-8% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Apr 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.25→30.195 Å / Num. obs: 61443 / % possible obs: 99.8 % / Redundancy: 6.7 % / CC1/2: 0.96 / Net I/σ(I): 6
Reflection shellResolution: 2.25→2.31 Å / Redundancy: 7.2 % / Num. unique obs: 4530 / CC1/2: 0.917 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→30.195 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.872 / SU B: 8.299 / SU ML: 0.202 / Cross valid method: FREE R-VALUE / ESU R: 0.312 / ESU R Free: 0.255
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2863 3091 5.032 %
Rwork0.2196 58332 -
all0.223 --
obs-61423 99.698 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.543 Å2
Baniso -1Baniso -2Baniso -3
1--0.468 Å2-0 Å2-0.846 Å2
2--1.276 Å20 Å2
3----0.682 Å2
Refinement stepCycle: LAST / Resolution: 2.25→30.195 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8040 0 76 724 8840
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0128264
X-RAY DIFFRACTIONr_bond_other_d0.0030.0167737
X-RAY DIFFRACTIONr_angle_refined_deg1.321.65311179
X-RAY DIFFRACTIONr_angle_other_deg0.4751.57317768
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.10151040
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.688550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.083101301
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.67310366
X-RAY DIFFRACTIONr_chiral_restr0.060.21260
X-RAY DIFFRACTIONr_chiral_restr_other0.3130.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029712
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021868
X-RAY DIFFRACTIONr_nbd_refined0.2180.21785
X-RAY DIFFRACTIONr_symmetry_nbd_other0.210.27614
X-RAY DIFFRACTIONr_nbtor_refined0.180.24041
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.24482
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2587
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0640.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2280.230
X-RAY DIFFRACTIONr_nbd_other0.2260.2157
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.170.227
X-RAY DIFFRACTIONr_mcbond_it1.9422.5384187
X-RAY DIFFRACTIONr_mcbond_other1.9422.5384187
X-RAY DIFFRACTIONr_mcangle_it3.1714.5425218
X-RAY DIFFRACTIONr_mcangle_other3.1714.5435219
X-RAY DIFFRACTIONr_scbond_it2.1812.5984077
X-RAY DIFFRACTIONr_scbond_other2.1812.5984078
X-RAY DIFFRACTIONr_scangle_it3.6174.725961
X-RAY DIFFRACTIONr_scangle_other3.6164.725962
X-RAY DIFFRACTIONr_lrange_it5.90725.1289433
X-RAY DIFFRACTIONr_lrange_other5.84625.0579268
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.25-2.3080.3362640.23942440.24445080.9310.9631000.223
2.308-2.3710.2912420.2341430.23343850.9430.9661000.211
2.371-2.4390.342210.27340900.27643110.9390.9611000.247
2.439-2.5140.3372020.29239630.29441660.9190.94999.9760.265
2.514-2.5960.3322170.2737960.27340170.9320.95699.90040.248
2.596-2.6860.3651850.26137280.26639140.9350.96599.97450.229
2.686-2.7870.2821740.21135610.21537350.9560.9731000.184
2.787-2.8990.3021750.21234550.21636310.9460.97399.97250.186
2.899-3.0270.361520.26633180.26934810.9290.96599.6840.225
3.027-3.1730.3491620.26231930.26633650.9210.95399.70280.236
3.173-3.3430.3451630.22929790.23431530.9340.96999.65110.203
3.343-3.5430.2871370.20428670.20830060.9570.98199.93350.195
3.543-3.7840.2841330.20127020.20428380.9560.98199.89430.194
3.784-4.0820.2471410.18224640.18626310.9670.98199.01180.174
4.082-4.4630.2191250.1623090.16424480.9730.98499.42810.156
4.463-4.9760.183880.15920930.1622010.9780.98699.09130.159
4.976-5.720.2161050.19818700.19919830.9750.98199.59660.198
5.72-6.9440.25960.2115630.21216700.9660.9899.34130.208
6.944-9.570.216790.18312290.18513200.9720.98199.09090.189
9.57-30.1950.259300.2157650.2178160.9650.97397.42650.227

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