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- PDB-3pgk: The structure of yeast phosphoglycerate kinase at 0.25 nm resolution -
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Open data
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Basic information
Entry | Database: PDB / ID: 3pgk | |||||||||
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Title | The structure of yeast phosphoglycerate kinase at 0.25 nm resolution | |||||||||
![]() | PHOSPHOGLYCERATE KINASE | |||||||||
![]() | TRANSFERASE / PHOSPHOTRANSFERASE(CARBOXYL AS ACCEPTOR) | |||||||||
Function / homology | ![]() Gluconeogenesis / Glycolysis / phosphoglycerate kinase / phosphoglycerate kinase activity / gluconeogenesis / glycolytic process / ADP binding / calmodulin binding / phosphorylation / mitochondrion ...Gluconeogenesis / Glycolysis / phosphoglycerate kinase / phosphoglycerate kinase activity / gluconeogenesis / glycolytic process / ADP binding / calmodulin binding / phosphorylation / mitochondrion / ATP binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Shaw, P.J. / Walker, N.P. / Watson, H.C. | |||||||||
![]() | ![]() Title: Sequence and structure of yeast phosphoglycerate kinase. Authors: Watson, H.C. / Walker, N.P. / Shaw, P.J. / Bryant, T.N. / Wendell, P.L. / Fothergill, L.A. / Perkins, R.E. / Conroy, S.C. / Dobson, M.J. / Tuite, M.F. #1: ![]() Title: The Complete Amino Acid Sequence of Yeast Phosphoglycerate Kinase Authors: Perkins, R.E. / Conroy, S.C. / Dunbar, B. / Fothergill, L.A. / Tuite, M.F. / Dobson, M.J. / Kingsman, S.M. / Kingsman, A.J. #2: ![]() Title: Sequence and Structure of Yeast Phosphoglycerate Kinase Authors: Watson, H.C. / Walker, N.P.C. / Shaw, P.J. / Bryant, T.N. / Wendell, P.L. / Fothergill, L.A. / Perkins, R.E. / Conroy, S.C. / Dobson, M.J. / Tuite, M.F. / Kingsman, A.J. / Kingsman, S.M. #3: ![]() Title: Structure of Yeast Phosphoglycerate Kinase Authors: Bryant, T.N. / Watson, H.C. / Wendell, P.L. #4: ![]() Title: Low Resolution Structure of Yeast Phosphoglycerate Kinase Authors: Wendell, P.L. / Bryant, T.N. / Watson, H.C. #5: ![]() Title: Crystallographic Study of Yeast Phosphoglycerate Kinase Authors: Watson, H.C. / Wendell, P.L. / Scopes, R.K. | |||||||||
History |
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Remark 700 | SHEET CAUTION. THE DEFINITION OF THE BEGINNING AND END OF HELICES AND SHEET STRANDS GIVEN BELOW ...SHEET CAUTION. THE DEFINITION OF THE BEGINNING AND END OF HELICES AND SHEET STRANDS GIVEN BELOW DEPENDS SOMEWHAT ON THE CRITERIA USED TO DEFINE A *GOOD* HYDROGEN BOND. TURNS LISTED BELOW ARE THOSE WHERE CA(1)-CA(4) IS LESS THAN 5.7 ANGSTROMS AND O(1)-N(4) IS LESS THAN 3.2 ANGSTROMS. FULL TURN DEFINITION MUST AWAIT FURTHER REFINEMENT. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 99.9 KB | Display | ![]() |
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PDB format | ![]() | 58.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 476.6 KB | Display | ![]() |
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Full document | ![]() | 721 KB | Display | |
Data in XML | ![]() | 54.9 KB | Display | |
Data in CIF | ![]() | 69.3 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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1 |
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Unit cell |
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Atom site foot note | 1: THIS ATOM MAY BE MAGNESIUM OR MANGANESE. |
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Components
#1: Protein | Mass: 44652.125 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P00560, phosphoglycerate kinase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-ATP / |
#4: Chemical | ChemComp-3PG / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.97 % |
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
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Processing
Refinement | Highest resolution: 2.5 Å | ||||||||||||
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Refinement step | Cycle: LAST / Highest resolution: 2.5 Å
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