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- PDB-4ukd: UMP/CMP KINASE FROM SLIME MOLD COMPLEXED WITH ADP, UDP, BERYLLIUM... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ukd | ||||||
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Title | UMP/CMP KINASE FROM SLIME MOLD COMPLEXED WITH ADP, UDP, BERYLLIUM FLUORIDE | ||||||
![]() | URIDYLMONOPHOSPHATE/CYTIDYLMONOPHOSPHATE KINASE | ||||||
![]() | TRANSFERASE / NUCLEOSIDE MONOPHOSPHATE KINASE / NMP KINASE / PHOSPHORYL TRANSFER / TRANSITION STATE ANALOG COMPLEX | ||||||
Function / homology | ![]() pyrimidine nucleobase salvage / nucleotide salvage / UMP/CMP kinase / CMP kinase activity / dCMP kinase activity / Interconversion of nucleotide di- and triphosphates / phosphotransferase activity, phosphate group as acceptor / CDP biosynthetic process / (d)CMP kinase activity / UMP kinase activity ...pyrimidine nucleobase salvage / nucleotide salvage / UMP/CMP kinase / CMP kinase activity / dCMP kinase activity / Interconversion of nucleotide di- and triphosphates / phosphotransferase activity, phosphate group as acceptor / CDP biosynthetic process / (d)CMP kinase activity / UMP kinase activity / adenylate kinase activity / UDP biosynthetic process / nucleoside diphosphate kinase activity / 'de novo' pyrimidine nucleobase biosynthetic process / phosphorylation / magnesium ion binding / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Schlichting, I. / Reinstein, J. | ||||||
![]() | ![]() Title: Structures of active conformations of UMP kinase from Dictyostelium discoideum suggest phosphoryl transfer is associative. Authors: Schlichting, I. / Reinstein, J. #1: ![]() Title: Crystal Structure of the Complex of Ump/Cmp Kinase from Dictyostelium Discoideum and the Bisubstrate Inhibitor P1-(5'-Adenosyl) P5-(5'-Uridyl) Pentaphosphate (Up5A) and Mg2+ at 2.2 A: ...Title: Crystal Structure of the Complex of Ump/Cmp Kinase from Dictyostelium Discoideum and the Bisubstrate Inhibitor P1-(5'-Adenosyl) P5-(5'-Uridyl) Pentaphosphate (Up5A) and Mg2+ at 2.2 A: Implications for Water-Mediated Specificity Authors: Scheffzek, K. / Kliche, W. / Wiesmuller, L. / Reinstein, J. #2: ![]() Title: Crystallization and Preliminary X-Ray Analysis of Ump/Cmp-Kinase from Dictyostelium Discoideum with the Specific Bisubstrate Inhibitor P1-(Adenosine 5')-P5-(Uridine 5')-Pentaphosphate (Up5A) Authors: Wiesmuller, L. / Scheffzek, K. / Kliche, W. / Goody, R.S. / Wittinghofer, A. / Reinstein, J. #3: ![]() Title: Cdna-Derived Sequence of Ump-Cmp Kinase from Dictyostelium Discoideum and Expression of the Enzyme in Escherichia Coli Authors: Wiesmuller, L. / Noegel, A.A. / Barzu, O. / Gerisch, G. / Schleicher, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 56.6 KB | Display | ![]() |
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PDB format | ![]() | 40.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 7.2 KB | Display | |
Data in CIF | ![]() | 10 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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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 21970.854 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 111 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/UDP.gif)
![](data/chem/img/BF2.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/UDP.gif)
![](data/chem/img/BF2.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MG / |
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#3: Chemical | ChemComp-ADP / |
#4: Chemical | ChemComp-UDP / |
#5: Chemical | ChemComp-BF2 / |
#6: Water | ChemComp-HOH / |
-Details
Nonpolymer details | BEF2 LINKS THE TWO NUCLEOTIDE |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.54 Å3/Da / Density % sol: 65 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 / Details: pH 8.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Oct 1, 1996 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→39 Å / Num. obs: 18420 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.084 |
Reflection shell | Resolution: 2→2.1 Å / Rmerge(I) obs: 0.366 / % possible all: 81 |
Reflection | *PLUS Num. measured all: 136023 |
Reflection shell | *PLUS % possible obs: 81 % |
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Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER / Resolution: 2→39 Å / σ(F): 0
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Displacement parameters | Biso mean: 28.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→39 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS % reflection Rfree: 5 % |