[English] 日本語
Yorodumi- PDB-1ndp: ADENOSINE 5'-DIPHOSPHATE BINDING AND THE ACTIVE SITE OF NUCLEOSID... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ndp | ||||||
---|---|---|---|---|---|---|---|
Title | ADENOSINE 5'-DIPHOSPHATE BINDING AND THE ACTIVE SITE OF NUCLEOSIDE DIPHOSPHATE KINASE | ||||||
Components | NUCLEOSIDE DIPHOSPHATE KINASENucleoside-diphosphate kinase | ||||||
Keywords | PHOSPHOTRANSFERASE | ||||||
Function / homology | Function and homology information dGTP biosynthetic process from dGDP / Azathioprine ADME / Ribavirin ADME / asexual reproduction / Interconversion of nucleotide di- and triphosphates / Neutrophil degranulation / nucleoside triphosphate biosynthetic process / negative regulation of pinocytosis / nucleoside-diphosphate kinase / UTP biosynthetic process ...dGTP biosynthetic process from dGDP / Azathioprine ADME / Ribavirin ADME / asexual reproduction / Interconversion of nucleotide di- and triphosphates / Neutrophil degranulation / nucleoside triphosphate biosynthetic process / negative regulation of pinocytosis / nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / negative regulation of exocytosis / negative regulation of phagocytosis / GTP biosynthetic process / nucleoside diphosphate kinase activity / translational elongation / phagocytic vesicle / secretory granule / response to bacterium / actin cytoskeleton organization / cytoskeleton / ribosome / G protein-coupled receptor signaling pathway / phosphorylation / ATP binding / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Dictyostelium discoideum (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | ||||||
Authors | Janin, J. / Morera, S. / Dumas, C. / Lascu, I. / Lebras, G. / Veron, M. | ||||||
Citation | Journal: Biochemistry / Year: 1994 Title: Adenosine 5'-diphosphate binding and the active site of nucleoside diphosphate kinase. Authors: Morera, S. / Lascu, I. / Dumas, C. / LeBras, G. / Briozzo, P. / Veron, M. / Janin, J. #1: Journal: To be Published Title: X-Ray Structure of Awd Nucleoside Diphosphate Kinase from Drosophila Authors: Chiadmi, M. / Morera, S. / Dumas, C. / Lebras, G. / Lascu, I. / Veron, M. / Janin, J. #2: 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. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ndp.cif.gz | 74.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ndp.ent.gz | 55.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ndp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nd/1ndp ftp://data.pdbj.org/pub/pdb/validation_reports/nd/1ndp | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 16816.336 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / References: UniProt: P22887, nucleoside-diphosphate kinase #2: Chemical | #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | Nonpolymer details | A MG++ ION (MG B 161) IS ASSOCIATED WITH ADP IN CHAIN B. IN CHAIN A, THE CORRESPONDING DENSITY IS ...A MG++ ION (MG B 161) IS ASSOCIATED | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.31 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Radiation | Scattering type: x-ray |
---|---|
Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.2 Å / Num. obs: 15408 / % possible obs: 88 % / Num. measured all: 31166 / Rmerge(I) obs: 0.074 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.2→10 Å / σ(F): 0 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.193 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 17.1 Å2 |