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- PDB-1gyq: CRYSTAL STRUCTURE OF GLYCOSOMAL GLYCERALDEHYDE FROM LEISHMANIA ME... -

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Basic information

Entry
Database: PDB / ID: 1gyq
TitleCRYSTAL STRUCTURE OF GLYCOSOMAL GLYCERALDEHYDE FROM LEISHMANIA MEXICANA IN COMPLEX WITH N6-BENZYL-NAD
ComponentsPROTEIN (GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE)
KeywordsOXIDOREDUCTASE / OXIDOREDUCTASE (ALDEHYDE(D)-NAD+(A))
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
N6-BENZYL-NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glyceraldehyde-3-phosphate dehydrogenase, glycosomal
Similarity search - Component
Biological speciesLeishmania mexicana (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsSuresh, S. / Hol, W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Structure-based design of submicromolar, biologically active inhibitors of trypanosomatid glyceraldehyde-3-phosphate dehydrogenase.
Authors: Aronov, A.M. / Suresh, S. / Buckner, F.S. / Van Voorhis, W.C. / Verlinde, C.L. / Opperdoes, F.R. / Hol, W.G. / Gelb, M.H.
History
DepositionMar 5, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 16, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: PROTEIN (GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE)
B: PROTEIN (GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE)
C: PROTEIN (GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE)
D: PROTEIN (GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,7878
Polymers154,7734
Non-polymers3,0144
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21200 Å2
ΔGint-127 kcal/mol
Surface area45030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.330, 125.810, 137.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.8165, 0.0233, -0.5769), (0.033, -0.9957, -0.0869), (-0.5764, -0.09, 0.8122)16.1114, 116.8066, 10.8465
2given(-0.9199, -0.3919, 0.0091), (-0.392, 0.9197, -0.0222), (0.0003, -0.024, -0.9997)26.4721, 5.9367, 48.4987
3given(0.738, 0.3519, 0.5758), (0.3594, -0.9271, 0.1059), (0.5712, 0.1288, -0.8107)-33.3552, 107.6277, 33.962
DetailsTHERE IS ONE 222 HOMOTETRAMER PER ASYMMETRIC UNIT RESULTING IN NON-CRYSTALLOGRAPHIC 222 SYMMETRY WITHIN THE ASYMMETRIC UNIT.

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Components

#1: Protein
PROTEIN (GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE) / GAPDH


Mass: 38693.129 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania mexicana (eukaryote) / Gene: GLYCERALDEHYDE-3-PHOSPHATEURCE 6 DEHYDROGENASE / Plasmid: PET-3A
Gene (production host): GLYCERALDEHYDE-3-PHOSPHATEURCE 6 DEHYDROGENASE
Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 PLYS S
References: UniProt: Q27890, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical
ChemComp-NBD / N6-BENZYL-NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 753.548 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H33N7O14P2

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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: 2.72 Å3/Da / Density % sol: 54.85 %
Description: DUE TO LIMITED RESOLUTION ONLY RIGID BODY REFINEMENT WAS DONE.
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.6
Details: 2UL OF SOLUTION CONTAINING 2.25 MG L. MEXICANA GAPDH, 1MM DDT, 1MM EDTA, 1MMPMSF 0.4 MM N6-BENZYL-NAD IN 10MM TRIETHANOLAMINE BUFFER PH 7.0 WAS MIXED WITH 1UL OF RESERVOIR SOLUTION ...Details: 2UL OF SOLUTION CONTAINING 2.25 MG L. MEXICANA GAPDH, 1MM DDT, 1MM EDTA, 1MMPMSF 0.4 MM N6-BENZYL-NAD IN 10MM TRIETHANOLAMINE BUFFER PH 7.0 WAS MIXED WITH 1UL OF RESERVOIR SOLUTION CONTAINING 25 %PEG5000MME, 100MM TRIS PH8.0 AND EQUILIBRATED IN SITTING DROP TRAYS, pH 7.6, VAPOR DIFFUSION, SITTING DROP
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.25 mg/mlprotein1drop
21 mMdithiothreitol1drop
31 mMEDTA1drop
41 mMphenylmethylsulfonyl fluoride1drop
50.4 mMN6-benzyl-NAD+1drop
610 mMtriethanolamine1drop
725 %mPEG50001reservoir
8100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 3.4→8 Å / Num. obs: 39118 / % possible obs: 84 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Rmerge(I) obs: 0.138 / Rsym value: 13.8 / Net I/σ(I): 5.9
Reflection shellResolution: 3.4→3.52 Å / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 1.8 / Rsym value: 43.3 / % possible all: 83
Reflection shell
*PLUS
% possible obs: 83 %

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Processing

Software
NameClassification
RAVEmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
RAVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GYP

1gyp


Highest resolution: 3.4 Å
Details: THE LIMITED RESOLUTION DID NOT PERMIT POSITIONAL OR B-FACTOR REFINEMENT. RIGID BODY REFINEMENT WAS DONE WITH X-PLOR
Refinement stepCycle: LAST / Highest resolution: 3.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10864 0 204 0 11068

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