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Yorodumi- PDB-1nue: X-RAY STRUCTURE OF NM23 HUMAN NUCLEOSIDE DIPHOSPHATE KINASE B COM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nue | ||||||
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Title | X-RAY STRUCTURE OF NM23 HUMAN NUCLEOSIDE DIPHOSPHATE KINASE B COMPLEXED WITH GDP AT 2 ANGSTROMS RESOLUTION | ||||||
Components | NUCLEOSIDE DIPHOSPHATE KINASE | ||||||
Keywords | PHOSPHOTRANSFERASE / NUCLEOSIDE TRIPHOSPHATE / NUCLEOSIDE DIPHOSPHATE | ||||||
Function / homology | Function and homology information regulation of epidermis development / nucleoside triphosphate biosynthetic process / protein histidine kinase activity / Ribavirin ADME / G-quadruplex DNA binding / nucleoside-diphosphate kinase / positive regulation of keratinocyte differentiation / Interconversion of nucleotide di- and triphosphates / CTP biosynthetic process / UTP biosynthetic process ...regulation of epidermis development / nucleoside triphosphate biosynthetic process / protein histidine kinase activity / Ribavirin ADME / G-quadruplex DNA binding / nucleoside-diphosphate kinase / positive regulation of keratinocyte differentiation / Interconversion of nucleotide di- and triphosphates / CTP biosynthetic process / UTP biosynthetic process / Azathioprine ADME / GTP biosynthetic process / nucleoside diphosphate kinase activity / histidine kinase / ruffle / cell periphery / positive regulation of epithelial cell proliferation / integrin-mediated signaling pathway / GDP binding / lamellipodium / regulation of apoptotic process / secretory granule lumen / ficolin-1-rich granule lumen / transcription coactivator activity / cell adhesion / Neutrophil degranulation / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / extracellular region / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Morera, S. / Lacombe, M.-L. / Yingwu, X. / Lebras, G. / Janin, J. | ||||||
Citation | Journal: Structure / Year: 1995 Title: X-ray structure of human nucleoside diphosphate kinase B complexed with GDP at 2 A resolution. Authors: Morera, S. / Lacombe, M.L. / Xu, Y. / LeBras, G. / Janin, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nue.cif.gz | 194.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nue.ent.gz | 158.4 KB | Display | PDB format |
PDBx/mmJSON format | 1nue.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nue_validation.pdf.gz | 731.8 KB | Display | wwPDB validaton report |
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Full document | 1nue_full_validation.pdf.gz | 736.3 KB | Display | |
Data in XML | 1nue_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 1nue_validation.cif.gz | 30.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nu/1nue ftp://data.pdbj.org/pub/pdb/validation_reports/nu/1nue | 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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-Components
#1: Protein | Mass: 17192.859 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P22392, nucleoside-diphosphate kinase #2: Chemical | #3: Chemical | ChemComp-GDP / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.81 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal | *PLUS Density % sol: 42 % | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8.4 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 66498 / % possible obs: 97.9 % |
Reflection | *PLUS Num. measured all: 418306 / Rmerge(I) obs: 0.106 |
-Processing
Software |
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Refinement | Resolution: 2→6 Å
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Refinement step | Cycle: LAST / Resolution: 2→6 Å
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Refine LS restraints |
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Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 17.6 Å2 |