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- PDB-1pgp: CRYSTALLOGRAPHIC STUDY OF COENZYME, COENZYME ANALOGUE AND SUBSTRA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1pgp | ||||||
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Title | CRYSTALLOGRAPHIC STUDY OF COENZYME, COENZYME ANALOGUE AND SUBSTRATE BINDING IN 6-PHOSPHOGLUCONATE DEHYDROGENASE: IMPLICATIONS FOR NADP SPECIFICITY AND THE ENZYME MECHANISM | ||||||
![]() | 6-PHOSPHOGLUCONATE DEHYDROGENASE | ||||||
![]() | OXIDOREDUCTASE (CHOH(D)-NADP+(A)) | ||||||
Function / homology | ![]() phosphogluconate 2-dehydrogenase activity / D-gluconate catabolic process / phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) / phosphogluconate dehydrogenase (decarboxylating) activity / pentose-phosphate shunt, oxidative branch / pentose-phosphate shunt / NADP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Adams, M.J. / Phillips, C. / Gover, S. / Naylor, C.E. | ||||||
![]() | ![]() Title: Crystallographic study of coenzyme, coenzyme analogue and substrate binding in 6-phosphogluconate dehydrogenase: implications for NADP specificity and the enzyme mechanism. Authors: Adams, M.J. / Ellis, G.H. / Gover, S. / Naylor, C.E. / Phillips, C. #1: ![]() Title: The Structure of 6-Phosphogluconate Dehydrogenase Refined at 2 Angstroms Resolution Authors: Phillips, C. / Gover, S. / Adams, M.J. #2: ![]() Title: The Structure of 6-Phosphogluconate Dehydrogenase Refined at 2.5 Angstroms Resolution Authors: Adams, M.J. / Gover, S. / Leaback, R. / Phillips, C. / Somers, D.O'N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 111.6 KB | Display | ![]() |
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PDB format | ![]() | 86.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 777.7 KB | Display | ![]() |
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Full document | ![]() | 781.8 KB | Display | |
Data in XML | ![]() | 23.4 KB | Display | |
Data in CIF | ![]() | 35 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO 67 2: LYS 459 - PRO 460 OMEGA = 142.91 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION | |||||||||||||||
Components on special symmetry positions |
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Components
#1: Protein | Mass: 52905.652 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P00349, phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) |
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#2: Sugar | ChemComp-6PG / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
Nonpolymer details | THE HET GROUP, 6-PHOSPHOGLU |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.87 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.5 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
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: 2.5 Å / Num. obs: 17989 / % possible obs: 92.8 % / Num. measured all: 44279 / Rmerge(I) obs: 0.0825 |
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Processing
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Refinement | Rfactor Rwork: 0.17 / Rfactor obs: 0.17 / Highest resolution: 2.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.5 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 20 Å / Rfactor obs: 0.17 / Rfactor Rwork: 0.17 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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