[English] 日本語
![](img/lk-miru.gif)
- PDB-1pgq: CRYSTALLOGRAPHIC STUDY OF COENZYME, COENZYME ANALOGUE AND SUBSTRA... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1pgq | ||||||
---|---|---|---|---|---|---|---|
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. | ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 112.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 86.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 764.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 773.2 KB | Display | |
Data in XML | ![]() | 24.2 KB | Display | |
Data in CIF | ![]() | 36.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
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) | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-2AM / | #4: Water | ChemComp-HOH / | Nonpolymer details | THE HET GROUP 2AM, 2'-ADENYLIC ACID, CARRIES A -- CHARGE. | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.87 % | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS pH: 6.5 / Method: batch method | |||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Radiation | Scattering type: x-ray |
---|---|
Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 3.17 Å / Num. obs: 8942 / % possible obs: 92.2 % / Num. measured all: 29208 / Rmerge(I) obs: 0.063 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Rfactor Rwork: 0.169 / Rfactor obs: 0.169 / Highest resolution: 3.17 Å Details: HET GROUP 2AM IS DESIGNATED 2'AMP IN THE JRNL REFERENCE. ATOMIC TEMPERATURE FACTORS AND SOLVENT OCCUPANCY AND POSITIONS WERE TAKEN FROM THE NATIVE STRUCTURE AT AN INTERMEDIATE STAGE OF ...Details: HET GROUP 2AM IS DESIGNATED 2'AMP IN THE JRNL REFERENCE. ATOMIC TEMPERATURE FACTORS AND SOLVENT OCCUPANCY AND POSITIONS WERE TAKEN FROM THE NATIVE STRUCTURE AT AN INTERMEDIATE STAGE OF REFINEMENT AND NOT REFINED. SOLVENT MOLECULES ARE ASSOCIATED WITH THE SAME MOLECULE AS THEIR CLOSEST OXYGEN OR NITROGEN NEIGHBOR; THIS BEST PRESERVES NETWORKS, BUT IN SOME INSTANCES HAS RESULTED IN THE NEAREST PROTEIN RESIDUE BEING THAT IN A SYMMETRY-RELATED MOLECULE. FOR SOME SOLVENT MOLECULES, THE DISTANCE TO THE CLOSEST OXYGEN OR NITROGEN NEIGHBOR IS MORE THAN 4 ANGSTROMS; THIS IS BECAUSE POORLY DEFINED SOLVENT SITES WERE OMITTED FROM NATIVE STRUCTURE REFINEMENT. THE CRITERIA APPLIED ARE DESCRIBED IN THE JRNL REFERENCE AND IN REFERENCE 1. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 3.17 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|