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- PDB-1gpd: STUDIES OF ASYMMETRY IN THE THREE-DIMENSIONAL STRUCTURE OF LOBSTE... -

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Entry
Database: PDB / ID: 1gpd
TitleSTUDIES OF ASYMMETRY IN THE THREE-DIMENSIONAL STRUCTURE OF LOBSTER D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
ComponentsD-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / OXIDO-REDUCTASE(ALDEHYDE/DONR / NAD/ACCPT) / OXIDO-REDUCTASE(ALDEHYDE-DONR / NAD-ACCPT) COMPLEX
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesHomarus americanus (American lobster)
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsMoras, D. / Olsen, K.W. / Sabesan, M.N. / Buehner, M. / Ford, G.C. / Rossmann, M.G.
Citation
Journal: J.Biol.Chem. / Year: 1975
Title: Studies of asymmetry in the three-dimensional structure of lobster D-glyceraldehyde-3-phosphate dehydrogenase.
Authors: Moras, D. / Olsen, K.W. / Sabesan, M.N. / Buehner, M. / Ford, G.C. / Rossmann, M.G.
#1: Journal: J.Mol.Biol. / Year: 1976
Title: Anion Binding Sites in the Active Center of D-Glyceraldehyde-3-Phosphate Dehydrogenase
Authors: Olsen, K.W. / Garavito, R.M. / Sabesan, M.N. / Rossmann, M.G.
#2: Journal: J.Mol.Biol. / Year: 1976
Title: Studies on Coenzyme Binding to Glyceraldehyde-3-Phosphate Dehydrogenase
Authors: Olsen, K.W. / Garavito, R.M. / Sabesan, M.N. / Rossmann, M.G.
#3: Journal: STRUCTURE AND CONFORMATION OF NUCLEIC ACIDS AND PROTEIN-NUCLEIC ACID INTERACTIONS : PROCEEDINGS OF THE FOURTH ANNUAL HARRY STEENBOCK SYMPOSIUM, JUNE 16-19, 1974, MADISON, WISCONSIN
Year: 1975
Title: A Comparison of the Binding and Function of Nad with Respect to Lactate Dehydrogenase and Glyceraldehyde-3-Phosphate Dehydrogenase
Authors: Rossmann, M.G.
#4: Journal: J.Biol.Chem. / Year: 1975
Title: Sequence Variability and Structure of D-Glyceraldehyde-3-Phosphate Dehydrogenase
Authors: Olsen, K.W. / Moras, D. / Rossmann, M.G. / Harris, J.I.
#5: Journal: J.Mol.Biol. / Year: 1974
Title: Three-Dimensional Structure of D-Glyceraldehyde-3-Phosphate Dehydrogenase
Authors: Buehner, M. / Ford, G.C. / Moras, D. / Olsen, K.W. / Rossmann, M.G.
#6: Journal: J.Mol.Biol. / Year: 1974
Title: Structure Determination of Crystalline Lobster D-Glyceraldehyde-3-Phosphate Dehydrogenase
Authors: Buehner, M. / Ford, G.C. / Moras, D. / Olsen, K.W. / Rossmann, M.G.
#7: Journal: Proc.Natl.Acad.Sci.USA / Year: 1973
Title: D-Glyceraldehyde-3-Phosphate Dehydrogenase,Three Dimensional Structure and Evolutionary Significance
Authors: Buehner, M. / Ford, G.C. / Moras, D. / Olsen, K.W. / Rossmann, M.G.
#8: Journal: Acta Crystallogr.,Sect.A / Year: 1975
Title: An Application of the Molecular Replacement Technique in Direct Space to a Known Protein Structure
Authors: Argos, P. / Ford, G.C. / Rossmann, M.G.
#9: Journal: Atlas of Macromolecular Structure on Microfiche / Year: 1976
#10: Journal: Atlas of Protein Sequence and Structure,Supplement 2
Year: 1976
History
DepositionJul 1, 1975Processing site: BNL
Revision 1.0Feb 17, 1977Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 29, 2014Group: Derived calculations
Revision 2.0Sep 27, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / atom_sites ...atom_site / atom_sites / cell / chem_comp_atom / chem_comp_bond / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_conn / struct_ncs_oper / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[1][2] / _atom_sites.fract_transf_matrix[1][3] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[2][3] / _atom_sites.fract_transf_matrix[3][1] / _atom_sites.fract_transf_matrix[3][2] / _atom_sites.fract_transf_matrix[3][3] / _atom_sites.fract_transf_vector[1] / _atom_sites.fract_transf_vector[2] / _atom_sites.fract_transf_vector[3] / _cell.Z_PDB / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[2][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][2] / _database_PDB_matrix.origx[3][3] / _database_PDB_matrix.origx_vector[1] / _database_PDB_matrix.origx_vector[2] / _database_PDB_matrix.origx_vector[3] / _pdbx_database_status.process_site / _pdbx_struct_assembly.details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_close_contact.dist / _pdbx_validate_planes.rmsd / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_oper.code / _struct_ncs_oper.matrix[1][1] / _struct_ncs_oper.matrix[1][2] / _struct_ncs_oper.matrix[1][3] / _struct_ncs_oper.matrix[2][1] / _struct_ncs_oper.matrix[2][2] / _struct_ncs_oper.matrix[2][3] / _struct_ncs_oper.matrix[3][1] / _struct_ncs_oper.matrix[3][2] / _struct_ncs_oper.matrix[3][3] / _struct_ncs_oper.vector[1] / _struct_ncs_oper.vector[2] / _struct_ncs_oper.vector[3] / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Details: Coordinates and associated ncs operations (if present) transformed into standard crystal frame
Provider: repository / Type: Remediation
Revision 2.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700SHEET THE SHEET SUBSTRUCTURE OF THE CATALYTIC DOMAIN IS BIFURCATED. TO REPRESENT THIS FEATURE ...SHEET THE SHEET SUBSTRUCTURE OF THE CATALYTIC DOMAIN IS BIFURCATED. TO REPRESENT THIS FEATURE REDUNDANT SHEETS ARE DEFINED FOR EACH OF THE TWO SUBUNITS. STRANDS 1-7 OF SHEETS GC1 AND RC1 ARE IDENTICAL TO STRANDS 1-7 OF SHEETS GC2 AND RC2.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
R: D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2758
Polymers71,5682
Non-polymers1,7076
Water00
1
G: D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
R: D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
hetero molecules

G: D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
R: D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,54916
Polymers143,1364
Non-polymers3,41312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Buried area5170 Å2
ΔGint-26 kcal/mol
Surface area28930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.000, 139.100, 80.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1generate(-0.17047561, -0.7483215, -0.64025496), (-0.74877992, -0.32451881, 0.57793364), (-0.64132256, 0.57854293, -0.50500557)96.24453, 70.94252, 41.77925
2given(0.00941452, 0.98799104, 0.15210148), (0.98861313, -0.03236886, 0.14896707), (0.15233541, 0.14910228, -0.97704567)38.22796, -40.04659, 6.4287
3given(-0.83893891, -0.23966954, 0.48815347), (-0.23983321, -0.64311232, -0.72690072), (0.48898716, -0.72764522, 0.48205124)115.57931, 59.02943, -9.1524

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Components

#1: Protein D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE


Mass: 35783.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homarus americanus (American lobster)
References: UniProt: P00357, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 5.84 Å3/Da / Density % sol: 78.95 %
Crystal grow
*PLUS
pH: 5.5 / Method: unknown
Details: (batch), took Watoson & Banaszak from Buehner et al., from original paper.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13.0 Mammonium sulfate11
20.001 MEDTA11
30.001 Mmercaptoethanol11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.9 Å / Num. obs: 13090 / Num. measured all: 33302

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Processing

RefinementHighest resolution: 2.9 Å
Refinement stepCycle: LAST / Highest resolution: 2.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5020 0 92 0 5112
Refinement
*PLUS
Highest resolution: 2.9 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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