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- PDB-1i32: LEISHMANIA MEXICANA GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE IN C... -

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Basic information

Entry
Database: PDB / ID: 1i32
TitleLEISHMANIA MEXICANA GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE IN COMPLEX WITH INHIBITORS
ComponentsGLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / enzyme / dehydrogenase
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glycosome / glycolytic process / glucose metabolic process / NAD binding / NADP binding / cytosol
Similarity search - Function
Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 ...Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NMD / Glyceraldehyde-3-phosphate dehydrogenase, glycosomal
Similarity search - Component
Biological speciesLeishmania mexicana (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSuresh, S. / Bressi, J.C. / Kennedy, K.J. / Verlinde, C.L.M.J. / Gelb, M.H. / Hol, W.G.J.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Conformational changes in Leishmania mexicana glyceraldehyde-3-phosphate dehydrogenase induced by designed inhibitors.
Authors: Suresh, S. / Bressi, J.C. / Kennedy, K.J. / Verlinde, C.L. / Gelb, M.H. / Hol, W.G.
History
DepositionFeb 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE
B: GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE
C: GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE
D: GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE
E: GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE
F: GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,14512
Polymers233,7216
Non-polymers3,4246
Water11,836657
1
A: GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE
B: GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE
C: GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE
D: GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,0968
Polymers155,8144
Non-polymers2,2824
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19730 Å2
ΔGint-85 kcal/mol
Surface area47420 Å2
MethodPISA
2
E: GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE
F: GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE
hetero molecules

E: GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE
F: GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,0968
Polymers155,8144
Non-polymers2,2824
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Unit cell
Length a, b, c (Å)80.385, 394.105, 70.963
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE / GAPDH


Mass: 38953.504 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania mexicana (eukaryote) / Production host: Escherichia coli (E. coli)
References: UniProt: Q27890, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical
ChemComp-NMD / N-NAPHTHALEN-1-YLMETHYL-2'-[3,5-DIMETHOXYBENZAMIDO]-2'-DEOXY-ADENOSINE


Mass: 570.596 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C30H30N6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 657 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.25
Details: PEG1000, 100mM TEA, 250mM NaCl, 5mM DTT, 1mM PMSF 15mM HEPES, pH 7.25, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlprotein1drop
215 mMHEPES1drop
3250 mM1dropNaCl
45 mMdithiothreitol1drop
51 mMPMSF1drop
634 mMinhibitor solution1drop
728 %(w/v)PEG10001reservoir
8100 mMTEA1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 16, 2000
RadiationMonochromator: synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→15 Å / Num. all: 65878 / Num. obs: 65878 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.18 % / Biso Wilson estimate: 47.7 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 29.3
Reflection shellResolution: 2.6→2.65 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.289 / % possible all: 71.7
Reflection
*PLUS
Lowest resolution: 15 Å / Num. measured all: 407373
Reflection shell
*PLUS
% possible obs: 71.7 % / Mean I/σ(I) obs: 4.7

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.256 3233 random
Rwork0.205 --
all0.205 65878 -
obs0.205 65878 -
Refinement stepCycle: LAST / Resolution: 2.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16290 0 252 657 17199
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.28
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 15 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.368 / Rfactor obs: 0.299

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