+
Open data
-
Basic information
Entry | Database: PDB / ID: 2ukd | ||||||
---|---|---|---|---|---|---|---|
Title | UMP/CMP KINASE FROM SLIME MOLD COMPLEXED WITH ADP, CMP | ||||||
![]() | URIDYLMONOPHOSPHATE/CYTIDYLMONOPHOSPHATE KINASE | ||||||
![]() | TRANSFERASE / NUCLEOSIDE MONOPHOSPHATE KINASE / NMP KINASE / PHOSPHORYL TRANSFER | ||||||
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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 56 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 40 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 11.1 KB | Display | |
Data in CIF | ![]() | 15.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 21970.854 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-ADP / |
#4: Chemical | ChemComp-C5P / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.53 Å3/Da / Density % sol: 65 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 8.5 / Details: pH 8.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 277 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1996 / Details: MIRRORS |
Radiation | Monochromator: Y / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.883 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→37 Å / Num. obs: 15558 / % possible obs: 94 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.074 |
Reflection shell | Resolution: 2.2→2.32 Å / Rmerge(I) obs: 0.221 / % possible all: 95 |
Reflection | *PLUS Num. measured all: 53982 |
Reflection shell | *PLUS % possible obs: 95 % |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: DIFFERENCE FOURIER / Resolution: 2.2→37 Å / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→37 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|