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- PDB-9iwc: High Resolution Crystal Structure of Glyceraldehyde-3-Phosphate D... -

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Entry
Database: PDB / ID: 9iwc
TitleHigh Resolution Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase from Saccharomyces cerevisiae Complexed with a Maleate Derivative
ComponentsGlyceraldehyde-3-phosphate dehydrogenase 3
KeywordsPROTEIN BINDING / covalent inhibitor
Function / homology
Function and homology information


Gluconeogenesis / Glycolysis / heme transport / melatonin binding / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / fungal-type cell wall / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / lipid droplet / reactive oxygen species metabolic process / gluconeogenesis ...Gluconeogenesis / Glycolysis / heme transport / melatonin binding / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / fungal-type cell wall / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / lipid droplet / reactive oxygen species metabolic process / gluconeogenesis / glycolytic process / NAD binding / NADP binding / mRNA binding / apoptotic process / heme binding / mitochondrion / RNA binding / nucleus / plasma membrane / cytosol / cytoplasm
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 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / Glyceraldehyde-3-phosphate dehydrogenase 3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsCao, H. / Zhang, X. / Ren, Y. / Wan, J.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22177036 China
National Natural Science Foundation of China (NSFC)22377030 China
National Natural Science Foundation of China (NSFC)22373039 China
CitationJournal: To Be Published
Title: High Resolution Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase from Saccharomyces cerevisiae Complexed with a Maleate Derivative
Authors: Cao, H. / Zhang, X. / Ren, Y. / Wan, J.
History
DepositionJul 25, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glyceraldehyde-3-phosphate dehydrogenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0402
Polymers36,8091
Non-polymers2311
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Glyceraldehyde-3-phosphate dehydrogenase 3
hetero molecules

A: Glyceraldehyde-3-phosphate dehydrogenase 3
hetero molecules

A: Glyceraldehyde-3-phosphate dehydrogenase 3
hetero molecules

A: Glyceraldehyde-3-phosphate dehydrogenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,1608
Polymers147,2354
Non-polymers9254
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_545y+1/2,x-1/2,-z+1/21
crystal symmetry operation10_655-x+1,-y,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
Buried area12690 Å2
ΔGint-74 kcal/mol
Surface area44700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.792, 115.792, 115.043
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-546-

HOH

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Components

#1: Protein Glyceraldehyde-3-phosphate dehydrogenase 3 / GAPDH 3 / Triose-phosphate dehydrogenase 1


Mass: 36808.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: TDH3, GPD3, YGR192C, G7576 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P00359, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical ChemComp-A1D98 / methyl 4-[(4-ethynylphenyl)amino]-4-oxidanylidene-butanoate


Mass: 231.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H13NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.62 Å3/Da / Density % sol: 53.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 25% v/v PEG 3350, 0.2M Ammonium acetate, pH 6.3, 0.5M sodium chloride, 0.1M Bis-Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.96→47.07 Å / Num. obs: 27081 / % possible obs: 90.32 % / Redundancy: 12.3 % / CC1/2: 0.998 / Net I/σ(I): 21.72
Reflection shellResolution: 1.965→2.035 Å / Num. unique obs: 2135 / CC1/2: 0.771

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→47.07 Å / SU ML: 0.26 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 28.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2431 1426 5.61 %
Rwork0.2123 --
obs0.2141 25397 90.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.96→47.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2459 0 17 123 2599
Refine LS restraintsType: f_plane_restr / Dev ideal: 0.008 / Number: 435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.040.36631020.36392033X-RAY DIFFRACTION78
2.04-2.120.37431030.32921890X-RAY DIFFRACTION72
2.12-2.210.37721160.29272360X-RAY DIFFRACTION89
2.21-2.330.34141130.26061945X-RAY DIFFRACTION74
2.33-2.480.29421230.24282513X-RAY DIFFRACTION95
2.48-2.670.28221580.21662558X-RAY DIFFRACTION97
2.67-2.930.27021990.21912564X-RAY DIFFRACTION98
2.94-3.360.24741620.20122644X-RAY DIFFRACTION99
3.36-4.230.21211520.19222689X-RAY DIFFRACTION100
4.23-47.070.20421980.18692775X-RAY DIFFRACTION99

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