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- PDB-2gd1: COENZYME-INDUCED CONFORMATIONAL CHANGES IN GLYCERALDEHYDE-3-PHOSP... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2gd1 | ||||||
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Title | COENZYME-INDUCED CONFORMATIONAL CHANGES IN GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM BACILLUS STEAROTHERMOPHILLUS | ||||||
![]() | APO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE | ||||||
![]() | OXIDOREDUCTASE(ALDEHYDE(D)-NAD(A)) | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Skarzynski, T. / Wonacott, A.J. | ||||||
![]() | ![]() Title: Coenzyme-induced conformational changes in glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus. Authors: Skarzynski, T. / Wonacott, A.J. #1: ![]() Title: Nucleotide Sequence Determination of the DNA Region Coding for Bacillus Stearothermophilus Glyceraldehyde-3-Phosphate Dehydrogenase and of the Flanking DNA Regions Required for its Expression in Escherichia Coli Authors: Branlant, C. / Oster, T. / Branlant, G. #2: ![]() Title: Structure of Holo-Glyceraldehyde-3-Phosphate Dehydrogenase from Bacillus Stearothermophilus at 1.8 Angstroms Resolution Authors: Skarzynski, T. / Moody, P.C.E. / Wonacott, A.J. #3: ![]() Title: Structural Evidence for Ligand-Induced Sequential Conformational Changes in Glyceraldehyde 3-Phosphate Dehydrogenase Authors: Leslie, A.G.W. / Wonacott, A.J. #4: ![]() Title: Coenzyme Binding in Crystals of Glyceraldehyde-3-Phosphate Dehydrogenase Authors: Leslie, A.G.W. / Wonacott, A.J. #5: ![]() Title: Glyceraldehyde-3-Phosphate Dehydrogenase Authors: Dalziel, K. / Mcferran, N.V. / Wonacott, A.J. #6: ![]() Title: Enzymes from Thermophilic Bacteria Authors: Walker, J.E. #7: ![]() Title: Sequence and Structure of D-Glyceraldehyde 3-Phosphate Dehydrogenase from Bacillus Stearothermophilus Authors: Biesecker, G. / Harris, J.I. / Thierry, J.C. / Walker, J.E. / Wonacott, A.J. #8: ![]() Title: Coenzyme Binding and Co-Operativity in D-Glyceraldehyde 3-Phosphate Dehydrogenase Authors: Biesecker, G. / Wonacott, A.J. #9: ![]() Title: Glyceraldehyde-3-Phosphate Dehydrogenase from Bacillus Stearothermophilus Authors: Suzuki, K. / Harris, J.I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 266.3 KB | Display | ![]() |
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PDB format | ![]() | 214.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.5 KB | Display | ![]() |
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Full document | ![]() | 501.4 KB | Display | |
Data in XML | ![]() | 57 KB | Display | |
Data in CIF | ![]() | 79.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Details | THE TRANSFORMATION PROVIDED ON THE *MTRIX 1* RECORDS BELOW YIELDS APPROXIMATE COORDINATES FOR CHAIN *P* WHEN APPLIED TO CHAIN *O*. THE TRANSFORMATION PROVIDED ON THE *MTRIX 2* RECORDS BELOW YIELDS APPROXIMATE COORDINATES FOR CHAIN *Q* WHEN APPLIED TO CHAIN *O*. THE TRANSFORMATION PROVIDED ON THE *MTRIX 3* RECORDS BELOW YIELDS APPROXIMATE COORDINATES FOR CHAIN *R* WHEN APPLIED TO CHAIN *O*. |
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Components
#1: Protein | Mass: 35991.047 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Cell line: 293 References: UniProt: P00362, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Sequence details | THE NUMBERING SCHEME USED IN THIS ENTRY MAXIMIZES THE HOMOLOGY BETWEEN SEQUENCES OF GAPDH FROM ...THE NUMBERING SCHEME USED IN THIS ENTRY MAXIMIZES THE HOMOLOGY BETWEEN SEQUENCES OF GAPDH FROM VARIOUS SOURCES. THE AMINO ACID SEQUENCE USED IS BASED ON THE GENE SEQUENCE (SEE REFERENCE 1 ABOVE) AND CONTAINS 20 DIFFERENCE | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.76 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.6 / Method: microdialysis / Details: referred to FEBS Lett.13.217-220 | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.5 Å / Num. obs: 55743 / % possible obs: 95.4 % / Rmerge(I) obs: 0.098 / Num. measured all: 183964 |
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Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Highest resolution: 2.5 Å /
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Refinement step | Cycle: LAST / Highest resolution: 2.5 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 7 Å / Rfactor obs: 0.177 / Highest resolution: 2.5 Å / Num. reflection all: 53315 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |