|Entry||Database: PDB / ID: 1ndk|
|Title||X-RAY STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE|
|Components||NUCLEOSIDE DIPHOSPHATE KINASENucleoside-diphosphate kinase|
|Function / homology|
Function and homology information
dGTP biosynthetic process from dGDP / dGDP phosphorylation / asexual reproduction / nucleoside triphosphate biosynthetic process / negative regulation of pinocytosis / negative regulation of exocytosis / nucleoside-diphosphate kinase / UTP biosynthetic process / negative regulation of phagocytosis / CTP biosynthetic process ...dGTP biosynthetic process from dGDP / dGDP phosphorylation / asexual reproduction / nucleoside triphosphate biosynthetic process / negative regulation of pinocytosis / negative regulation of exocytosis / nucleoside-diphosphate kinase / UTP biosynthetic process / negative regulation of phagocytosis / CTP biosynthetic process / GTP biosynthetic process / translational elongation / nucleoside diphosphate kinase activity / phagocytic vesicle / response to bacterium / secretory granule / actin cytoskeleton organization / ribosome / cytoskeleton / G protein-coupled receptor signaling pathway / ATP binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinases active site. / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / NDK / Nucleoside diphosphate kinase-like domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Nucleoside diphosphate kinase, cytosolic
Similarity search - Component
|Biological species||Dictyostelium discoideum (eukaryote)|
|Method||X-RAY DIFFRACTION / Resolution: 2.2 Å|
|Authors||Janin, J. / Dumas, C. / Morera, S. / Lascu, I. / Veron, M.|
|Citation||Journal: EMBO J. / Year: 1992|
Title: X-ray structure of nucleoside diphosphate kinase.
Authors: Dumas, C. / Lascu, I. / Morera, S. / Glaser, P. / Fourme, R. / Wallet, V. / Lacombe, M.L. / Veron, M. / Janin, J.
|Structure viewer||Molecule: |
Downloads & links
A: NUCLEOSIDE DIPHOSPHATE KINASE
A: NUCLEOSIDE DIPHOSPHATE KINASEx 6
|#1: Protein|| |
Mass: 16781.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / References: UniProt: P22887, nucleoside-diphosphate kinase
|#2: Water|| ChemComp-HOH / |
|Experiment||Method: X-RAY DIFFRACTION|
|Crystal||Density Matthews: 2.44 Å3/Da / Density % sol: 49.63 %|
*PLUSpH: 7.2 / Method: vapor diffusion, hanging drop
|Components of the solutions|
|Radiation||Scattering type: x-ray|
|Radiation wavelength||Relative weight: 1|
*PLUSHighest resolution: 2.2 Å / Lowest resolution: 20 Å / Num. obs: 9012 / % possible obs: 99.3 % / Num. measured all: 82562 / Rmerge(I) obs: 0.046
|Refinement||Rfactor Rwork: 0.203 / Rfactor obs: 0.203 / Highest resolution: 2.2 Å|
Details: NO DENSITY IS SEEN FOR RESIDUES 1 - 7. DENSITY FOR RESIDUE 8 IS POOR.
|Refinement step||Cycle: LAST / Highest resolution: 2.2 Å|
|Refine LS restraints|
*PLUSHighest resolution: 2.2 Å / Lowest resolution: 7 Å / Num. reflection obs: 8697 / Rfactor obs: 0.203
|Refine LS restraints|
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