+Open data
-Basic information
Entry | Database: PDB / ID: 1ndl | ||||||
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Title | THE AWD NUCLEOTIDE DIPHOSPHATE KINASE FROM DROSOPHILA | ||||||
Components | NUCLEOSIDE DIPHOSPHATE KINASE | ||||||
Keywords | PHOSPHOTRANSFERASE | ||||||
Function / homology | Function and homology information regulation of tube architecture, open tracheal system / Azathioprine ADME / Ribavirin ADME / establishment or maintenance of polarity of follicular epithelium / open tracheal system development / epithelial cell migration, open tracheal system / Interconversion of nucleotide di- and triphosphates / nuclear microtubule / Neutrophil degranulation / nucleoside-diphosphate kinase ...regulation of tube architecture, open tracheal system / Azathioprine ADME / Ribavirin ADME / establishment or maintenance of polarity of follicular epithelium / open tracheal system development / epithelial cell migration, open tracheal system / Interconversion of nucleotide di- and triphosphates / nuclear microtubule / Neutrophil degranulation / nucleoside-diphosphate kinase / nucleotide metabolic process / UTP biosynthetic process / CTP biosynthetic process / adherens junction organization / GTP biosynthetic process / nucleoside diphosphate kinase activity / microtubule-based process / kinase activity / mitotic cell cycle / microtubule binding / microtubule / GTP binding / magnesium ion binding / ATP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.4 Å | ||||||
Authors | Janin, J. / Chiadmi, M. / Dumas, C. / Lascu, I. / Lebras, G. / Morera, S. / Veron, M. | ||||||
Citation | Journal: Structure / Year: 1993 Title: Crystal structure of the Awd nucleotide diphosphate kinase from Drosophila. Authors: Chiadmi, M. / Morera, S. / Lascu, I. / Dumas, C. / Le Bras, G. / Veron, M. / Janin, J. #1: 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. #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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ndl.cif.gz | 105.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ndl.ent.gz | 82.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ndl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ndl_validation.pdf.gz | 376.1 KB | Display | wwPDB validaton report |
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Full document | 1ndl_full_validation.pdf.gz | 386.4 KB | Display | |
Data in XML | 1ndl_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 1ndl_validation.cif.gz | 18.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nd/1ndl ftp://data.pdbj.org/pub/pdb/validation_reports/nd/1ndl | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: ELECTRON DENSITY IS ABSENT FOR MET 1 AND POOR FOR ALA 2 IN ALL THREE CHAINS. | ||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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Details | THE TRANSFORMATION PRESENTED ON *MTRIX 3* RECORDS BELOW WILL GENERATE THE HEXAMER FROM THE TRIMER PRESENTED IN THE ENTRY. |
-Components
#1: Protein | Mass: 17190.852 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / References: UniProt: P08879, nucleoside-diphosphate kinase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.69 Å3/Da / Density % sol: 66.65 % |
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.4→10 Å / σ(F): 1 /
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Refinement step | Cycle: LAST / Resolution: 2.4→10 Å
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Refine LS restraints |
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