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Yorodumi- PDB-1jkl: 1.6A X-RAY STRUCTURE OF BINARY COMPLEX OF A CATALYTIC DOMAIN OF D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jkl | ||||||
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Title | 1.6A X-RAY STRUCTURE OF BINARY COMPLEX OF A CATALYTIC DOMAIN OF DEATH-ASSOCIATED PROTEIN KINASE WITH ATP ANALOGUE | ||||||
Components | DEATH-ASSOCIATED PROTEIN KINASE | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information cellular response to hydroperoxide / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / defense response to tumor cell / Caspase activation via Dependence Receptors in the absence of ligand / calmodulin-dependent protein kinase activity / syntaxin-1 binding / regulation of NMDA receptor activity / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process ...cellular response to hydroperoxide / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / defense response to tumor cell / Caspase activation via Dependence Receptors in the absence of ligand / calmodulin-dependent protein kinase activity / syntaxin-1 binding / regulation of NMDA receptor activity / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of autophagy / regulation of autophagy / apoptotic signaling pathway / cellular response to type II interferon / actin cytoskeleton / regulation of apoptotic process / negative regulation of translation / postsynaptic density / protein autophosphorylation / calmodulin binding / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / apoptotic process / GTP binding / negative regulation of apoptotic process / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.62 Å | ||||||
Authors | Tereshko, V. / Teplova, M. / Brunzelle, J. / Watterson, D.M. / Egli, M. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2001 Title: Crystal structures of the catalytic domain of human protein kinase associated with apoptosis and tumor suppression. Authors: Tereshko, V. / Teplova, M. / Brunzelle, J. / Watterson, D.M. / Egli, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jkl.cif.gz | 75.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jkl.ent.gz | 55 KB | Display | PDB format |
PDBx/mmJSON format | 1jkl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jk/1jkl ftp://data.pdbj.org/pub/pdb/validation_reports/jk/1jkl | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33794.367 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, PROTEIN KINASE DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) References: UniProt: P53355, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor |
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#2: Chemical | ChemComp-ANP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.28 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: PROTEIN, AMPPNP, AMMONIUM SULFATE, TRIS-HL, pH 7.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1.2562 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 1, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2562 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→20 Å / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.037 |
Reflection shell | Resolution: 1.62→1.68 Å / Rmerge(I) obs: 0.36 / % possible all: 94.2 |
Reflection | *PLUS Highest resolution: 1.62 Å / Lowest resolution: 20 Å / Num. obs: 32120 / Rmerge(I) obs: 0.037 |
Reflection shell | *PLUS % possible obs: 94.2 % / Num. unique obs: 2936 / Rmerge(I) obs: 0.27 |
-Processing
Software |
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Refinement | Resolution: 1.62→19.93 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 791907.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.8516 Å2 / ksol: 0.393044 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.62→19.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.62→1.72 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Refinement | *PLUS Rfactor obs: 0.201 / Rfactor Rfree: 0.218 / Rfactor Rwork: 0.201 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.295 / Rfactor Rwork: 0.262 |