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Yorodumi- PDB-1gpd: STUDIES OF ASYMMETRY IN THE THREE-DIMENSIONAL STRUCTURE OF LOBSTE... -
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-Basic information
Entry | Database: PDB / ID: 1gpd | |||||||||
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Title | STUDIES OF ASYMMETRY IN THE THREE-DIMENSIONAL STRUCTURE OF LOBSTER D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE | |||||||||
Components | D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE | |||||||||
Keywords | OXIDOREDUCTASE / 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 / cytoplasm Similarity search - Function | |||||||||
Biological species | Homarus americanus (American lobster) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.9 Å | |||||||||
Authors | Moras, 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. | |||||||||
History |
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Remark 700 | SHEET 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gpd.cif.gz | 129.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gpd.ent.gz | 92.2 KB | Display | PDB format |
PDBx/mmJSON format | 1gpd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gp/1gpd ftp://data.pdbj.org/pub/pdb/validation_reports/gp/1gpd | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | 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 | #3: Chemical | ChemComp-PO4 / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 5.84 Å3/Da / Density % sol: 78.95 % | ||||||||||||||||||||
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Crystal grow | *PLUS pH: 5.5 / Method: unknownDetails: (batch), took Watoson & Banaszak from Buehner et al., from original paper. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.9 Å / Num. obs: 13090 / Num. measured all: 33302 |
-Processing
Refinement | Highest resolution: 2.9 Å | ||||||||||||
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Refinement step | Cycle: LAST / Highest resolution: 2.9 Å
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Refinement | *PLUS Highest resolution: 2.9 Å | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |