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- PDB-5c7o: Structure of human testis-specific glyceraldehyde-3-phosphate deh... -

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Basic information

Entry
Database: PDB / ID: 5c7o
TitleStructure of human testis-specific glyceraldehyde-3-phosphate dehydrogenase holo form with NAD+
ComponentsGlyceraldehyde-3-phosphate dehydrogenase, testis-specificGlyceraldehyde 3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / human sperm GAPDH metabolic enzyme sperm specific with NAD+ cofactor
Function / homology
Function and homology information


flagellated sperm motility / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / Gluconeogenesis / Glycolysis / Association of TriC/CCT with target proteins during biosynthesis / positive regulation of glycolytic process / glycolytic process / glucose metabolic process / NAD binding ...flagellated sperm motility / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / Gluconeogenesis / Glycolysis / Association of TriC/CCT with target proteins during biosynthesis / positive regulation of glycolytic process / glycolytic process / glucose metabolic process / NAD binding / NADP binding / nucleus / cytosol
Similarity search - Function
Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / 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, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glyceraldehyde-3-phosphate dehydrogenase, testis-specific
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.729 Å
AuthorsBetts, L. / Machius, M. / Danshina, P. / O'Brien, D.
CitationJournal: Mol. Hum. Reprod. / Year: 2016
Title: Structural analyses to identify selective inhibitors of glyceraldehyde 3-phosphate dehydrogenase-S, a sperm-specific glycolytic enzyme.
Authors: Danshina, P.V. / Qu, W. / Temple, B.R. / Rojas, R.J. / Miley, M.J. / Machius, M. / Betts, L. / O'Brien, D.A.
History
DepositionJun 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Sep 27, 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 / pdbx_struct_oper_list / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
O: Glyceraldehyde-3-phosphate dehydrogenase, testis-specific
P: Glyceraldehyde-3-phosphate dehydrogenase, testis-specific
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8546
Polymers73,3352
Non-polymers1,5194
Water11,331629
1
O: Glyceraldehyde-3-phosphate dehydrogenase, testis-specific
P: Glyceraldehyde-3-phosphate dehydrogenase, testis-specific
hetero molecules

O: Glyceraldehyde-3-phosphate dehydrogenase, testis-specific
P: Glyceraldehyde-3-phosphate dehydrogenase, testis-specific
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,70912
Polymers146,6714
Non-polymers3,0388
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area21620 Å2
ΔGint-182 kcal/mol
Surface area42250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.442, 71.741, 80.844
Angle α, β, γ (deg.)90.000, 123.010, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11O-275-

HIS

21O-275-

HIS

31P-275-

HIS

41O-919-

HOH

51P-890-

HOH

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Components

#1: Protein Glyceraldehyde-3-phosphate dehydrogenase, testis-specific / Glyceraldehyde 3-phosphate dehydrogenase / Spermatogenic cell-specific glyceraldehyde 3-phosphate dehydrogenase 2 / GAPDH-2 / Spermatogenic ...Spermatogenic cell-specific glyceraldehyde 3-phosphate dehydrogenase 2 / GAPDH-2 / Spermatogenic glyceraldehyde-3-phosphate dehydrogenase


Mass: 36667.746 Da / Num. of mol.: 2 / Fragment: unp residues 74-407
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GAPDHS, GAPD2, GAPDH2, GAPDS, HSD-35, HSD35 / Production host: Escherichia coli (E. coli)
References: UniProt: O14556, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 629 / 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: 48.74 %
Crystal growTemperature: 273 K / Method: vapor diffusion
Details: 1:1 mixture of protein:NAD+ complex at 10 mg/mL with 0.2 M sodium nitrate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.0746 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0746 Å / Relative weight: 1
ReflectionResolution: 1.73→31.71 Å / Num. obs: 68115 / % possible obs: 93.9 % / Redundancy: 4.2 % / Net I/σ(I): 19.2

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H9E

3h9e


Resolution: 1.729→31.706 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1664 2013 2.96 %
Rwork0.1371 66102 -
obs0.138 68115 93.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.93 Å2 / Biso mean: 26.8695 Å2 / Biso min: 10.59 Å2
Refinement stepCycle: final / Resolution: 1.729→31.706 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5124 0 150 629 5903
Biso mean--27.66 35.2 -
Num. residues----670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055455
X-RAY DIFFRACTIONf_angle_d1.0267452
X-RAY DIFFRACTIONf_chiral_restr0.039833
X-RAY DIFFRACTIONf_plane_restr0.006957
X-RAY DIFFRACTIONf_dihedral_angle_d13.8072002
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7288-1.7720.2118770.18942515259250
1.772-1.81990.2391180.19453843396178
1.8199-1.87350.18731360.18164553468991
1.8735-1.93390.1971590.17114862502197
1.9339-2.0030.19741510.159649995150100
2.003-2.08320.18141510.148249825133100
2.0832-2.1780.18551550.14350245179100
2.178-2.29280.16481540.134950115165100
2.2928-2.43640.16611490.133749995148100
2.4364-2.62440.16481500.137650345184100
2.6244-2.88840.1551510.136950465197100
2.8884-3.3060.16771480.137250155163100
3.306-4.16370.14141540.120350705224100
4.1637-31.71080.16021600.122751495309100

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