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- PDB-1x0x: Co-Structure of Homo Sapiens Glycerol-3-Phosphate Dehydrogenase 1... -

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Basic information

Entry
Database: PDB / ID: 1x0x
TitleCo-Structure of Homo Sapiens Glycerol-3-Phosphate Dehydrogenase 1 complex with NAD
ComponentsGlycerol-3-phosphate dehydrogenase [NAD+], cytoplasmic
KeywordsOXIDOREDUCTASE / NAD / co-enzyme / GPD1
Function / homology
Function and homology information


glycerophosphate shuttle / glycerolipid metabolic process / glycerol-3-phosphate dehydrogenase (quinone) activity / glycerol-3-phosphate dehydrogenase (NAD+) / glycerol-3-phosphate dehydrogenase (NAD+) activity / glycerol-3-phosphate catabolic process / glycerol-3-phosphate metabolic process / NADH oxidation / Synthesis of PA / cellular response to cAMP ...glycerophosphate shuttle / glycerolipid metabolic process / glycerol-3-phosphate dehydrogenase (quinone) activity / glycerol-3-phosphate dehydrogenase (NAD+) / glycerol-3-phosphate dehydrogenase (NAD+) activity / glycerol-3-phosphate catabolic process / glycerol-3-phosphate metabolic process / NADH oxidation / Synthesis of PA / cellular response to cAMP / positive regulation of glycolytic process / gluconeogenesis / NAD binding / cellular response to tumor necrosis factor / protein homodimerization activity / extracellular exosome / cytosol
Similarity search - Function
Glycerol-3-phosphate dehydrogenase, NAD-dependent, eukaryotic / NAD-dependent glycerol-3-phosphate dehydrogenase signature. / Glycerol-3-phosphate dehydrogenase, NAD-dependent, C-terminal / Glycerol-3-phosphate dehydrogenase, NAD-dependent / Glycerol-3-phosphate dehydrogenase, NAD-dependent, N-terminal / NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus / NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 ...Glycerol-3-phosphate dehydrogenase, NAD-dependent, eukaryotic / NAD-dependent glycerol-3-phosphate dehydrogenase signature. / Glycerol-3-phosphate dehydrogenase, NAD-dependent, C-terminal / Glycerol-3-phosphate dehydrogenase, NAD-dependent / Glycerol-3-phosphate dehydrogenase, NAD-dependent, N-terminal / NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus / NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glycerol-3-phosphate dehydrogenase [NAD(+)], cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsRao, Z. / Ou, X.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structures of Human Glycerol 3-phosphate Dehydrogenase 1 (GPD1)
Authors: Ou, X. / Ji, C. / Han, X. / Zhao, X. / Li, X. / Mao, Y. / Wong, L.L. / Bartlam, M. / Rao, Z.
History
DepositionMar 31, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 11, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Glycerol-3-phosphate dehydrogenase [NAD+], cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1647
Polymers38,0201
Non-polymers1,1446
Water3,783210
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Glycerol-3-phosphate dehydrogenase [NAD+], cytoplasmic
hetero molecules

A: Glycerol-3-phosphate dehydrogenase [NAD+], cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,32714
Polymers76,0402
Non-polymers2,28712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_553x,-y+1/2,-z-7/41
Buried area7860 Å2
ΔGint-161 kcal/mol
Surface area25320 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)116.599, 116.599, 153.742
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Glycerol-3-phosphate dehydrogenase [NAD+], cytoplasmic / GPD-C / GPDH-C


Mass: 38020.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3(BL21)
References: UniProt: P21695, glycerol-3-phosphate dehydrogenase (NAD+)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 3.4 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M tri-Sodium Citrate dihydrate, 0.5M Ammonium Sulfate, 1.0M Lithium Sulfate monohydrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. all: 26614 / Num. obs: 26614 / % possible obs: 99.99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.75→2.85 Å / % possible all: 99.99

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.239 656 RANDOM
Rwork0.178 --
all0.188 14124 -
obs0.182 13788 -
Refinement stepCycle: LAST / Resolution: 2.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2638 0 69 210 2917
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.12
X-RAY DIFFRACTIONc_angle_deg1.59

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