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- PDB-1nsk: THE CRYSTAL STRUCTURE OF A HUMAN NUCLEOSIDE DIPHOSPHATE KINASE, N... -
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Basic information
Entry | Database: PDB / ID: 1nsk | ||||||
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Title | THE CRYSTAL STRUCTURE OF A HUMAN NUCLEOSIDE DIPHOSPHATE KINASE, NM23-H2 | ||||||
![]() | NUCLEOSIDE DIPHOSPHATE KINASE | ||||||
![]() | PHOSPHOTRANSFERASE (PO4 AS ACCEPTOR) | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() | ||||||
![]() | Williams, R.L. / Perisic, O. | ||||||
![]() | ![]() Title: The crystal structure of a human nucleoside diphosphate kinase, NM23-H2. Authors: Webb, P.A. / Perisic, O. / Mendola, C.E. / Backer, J.M. / Williams, R.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 178.7 KB | Display | ![]() |
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PDB format | ![]() | 148.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 469.9 KB | Display | ![]() |
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Full document | ![]() | 485.8 KB | Display | |
Data in XML | ![]() | 32.7 KB | Display | |
Data in CIF | ![]() | 43.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 17324.055 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.76 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 Å |
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Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→25 Å / Num. obs: 29553 / % possible obs: 92.8 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.087 |
Reflection | *PLUS Rmerge(I) obs: 0.087 |
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Processing
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Refinement | Resolution: 2.8→6 Å / σ(F): 0
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Displacement parameters | Biso mean: 29.63 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→6 Å
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Refine LS restraints |
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