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Yorodumi- PDB-4idv: Crystal Structure of NIK with compound 4-{3-[2-amino-5-(2-methoxy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4idv | ||||||
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Title | Crystal Structure of NIK with compound 4-{3-[2-amino-5-(2-methoxyethoxy)pyrimidin-4-yl]-1H-indol-5-yl}-2-methylbut-3-yn-2-ol (13V) | ||||||
Components | Mitogen-activated protein kinase kinase kinase 14 | ||||||
Keywords | Transferase/Transferase Inhibitor / NIK / Nuclear factor (NF)-kB / p100 processing / 2-aminopyrimidine / Transferase-Transferase Inhibitor complex | ||||||
Function / homology | Function and homology information TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / mitogen-activated protein kinase kinase kinase / non-canonical NF-kappaB signal transduction / CD28 dependent PI3K/Akt signaling / MAP kinase kinase kinase activity / canonical NF-kappaB signal transduction / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / Dectin-1 mediated noncanonical NF-kB signaling / fibrillar center ...TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / mitogen-activated protein kinase kinase kinase / non-canonical NF-kappaB signal transduction / CD28 dependent PI3K/Akt signaling / MAP kinase kinase kinase activity / canonical NF-kappaB signal transduction / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / Dectin-1 mediated noncanonical NF-kB signaling / fibrillar center / cellular response to mechanical stimulus / defense response to virus / protein kinase activity / immune response / phosphorylation / protein serine kinase activity / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / nucleoplasm / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Liu, J. / Sudom, A. / Wang, Z. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2013 Title: Inhibiting NF-KB-inducing kinase (NIK): Discovery, structure-based design, synthesis, structure activity relationship, and co-crystal structures Authors: Li, K. / McGee, L.R. / Fisher, B. / Sudom, A. / Liu, J. / Rubenstein, S.M. / Anwer, M.K. / Cushing, T.D. / Shin, Y. / Ayres, M. / Lee, F. / Eksterowicz, J. / Faulder, P. / Waszkowycz, B. / ...Authors: Li, K. / McGee, L.R. / Fisher, B. / Sudom, A. / Liu, J. / Rubenstein, S.M. / Anwer, M.K. / Cushing, T.D. / Shin, Y. / Ayres, M. / Lee, F. / Eksterowicz, J. / Faulder, P. / Waszkowycz, B. / Plotnikova, O. / Farrelly, E. / Xiao, S.H. / Chen, G. / Wang, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4idv.cif.gz | 266 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4idv.ent.gz | 216.1 KB | Display | PDB format |
PDBx/mmJSON format | 4idv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/4idv ftp://data.pdbj.org/pub/pdb/validation_reports/id/4idv | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 39145.703 Da / Num. of mol.: 4 / Fragment: UNP residues 330-680 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAP3K14, NIK References: UniProt: Q99558, mitogen-activated protein kinase kinase kinase #2: Chemical | ChemComp-13V / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.35 % |
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-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.9→127.35 Å / Num. obs: 31375 / % possible obs: 81.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.144 / Rsym value: 0.144 / Net I/σ(I): 9.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→32.14 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.853 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 16.542 / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.508 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||
Displacement parameters | Biso max: 158.49 Å2 / Biso mean: 40.3343 Å2 / Biso min: 3.22 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→32.14 Å
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LS refinement shell | Resolution: 2.9→2.975 Å / Total num. of bins used: 20
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