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- PDB-1ihy: GAPDH complexed with ADP-ribose -

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Basic information

Entry
Database: PDB / ID: 1ihy
TitleGAPDH complexed with ADP-ribose
ComponentsGLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / GAPDH / D-glyceraldehyde-3-phosphate dehydrogenase / ADP-ribose
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / 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
ADENOSINE-5-DIPHOSPHORIBOSE / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesPalinurus versicolor (painted spiny lobster)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsShen, Y.-Q. / Song, S.-Y. / Lin, Z.-J.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Structures of D-glyceraldehyde-3-phosphate dehydrogenase complexed with coenzyme analogues.
Authors: Shen, Y.Q. / Song, S.Y. / Lin, Z.J.
#1: Journal: J.Struct.Biol. / Year: 2000
Title: Structure of apo-D-glyceraldehyde-3-phosphate dehydrogenase from Palinurus versicolor
Authors: Shen, Y.-Q. / Li, J. / Song, S.-Y. / Lin, Z.-J.
History
DepositionApr 20, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 31, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,42616
Polymers143,4204
Non-polymers3,00612
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20400 Å2
ΔGint-279 kcal/mol
Surface area42530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.800, 100.350, 128.310
Angle α, β, γ (deg.)90.00, 110.28, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE / GAPDH


Mass: 35855.109 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Palinurus versicolor (painted spiny lobster)
Tissue: TAIL MUSCLE
References: UniProt: P56649, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 3.22 Å3/Da / Density % sol: 61.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: ammonium sulphate, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Details: Shen, Y.O., (2000) Chin. Sci. Bull., 45, 1199.

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SEALED TUBE / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 35186 / % possible obs: 97.2 % / Redundancy: 6 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.138 / Net I/σ(I): 7
Reflection shellResolution: 3→3.11 Å / Redundancy: 3 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3 / Num. unique all: 3566 / % possible all: 98.5
Reflection
*PLUS
Lowest resolution: 30 Å / % possible obs: 97 % / Num. measured all: 92755
Reflection shell
*PLUS
Highest resolution: 3 Å / % possible obs: 98.5 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→24.37 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 4824928.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.207 3267 10 %RANDOM
Rwork0.176 ---
obs0.176 32741 90 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.12 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso mean: 29.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.38 Å20 Å22.9 Å2
2--3.95 Å20 Å2
3----6.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-6 Å
Luzzati sigma a0.4 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 3→24.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10048 0 184 85 10317
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it2.22
X-RAY DIFFRACTIONc_scbond_it2.182
X-RAY DIFFRACTIONc_scangle_it3.432.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.291 487 9.4 %
Rwork0.245 4689 -
obs--85.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4NEWPARAM.SO4NEWTOPO.SO4
X-RAY DIFFRACTION5PARAM.ADRTOPO.ADR
Refinement
*PLUS
Rfactor Rfree: 0.196 / Rfactor Rwork: 0.167
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8

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