+Open data
-Basic information
Entry | Database: PDB / ID: 1skj | ||||||
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Title | COCRYSTAL STRUCTURE OF UREA-SUBSTITUTED PHOSPHOPEPTIDE COMPLEX | ||||||
Components | PP60 V-SRC TYROSINE KINASE TRANSFORMING PROTEIN | ||||||
Keywords | TYROSINE-PROTEIN KINASE / V-SRC SH2 DOMAIN / PHOSPHOTYROSINE RECOGNITION DOMAIN / PP60 SRC SH2 DOMAIN / PEPTIDOMIMETIC / UREIDO | ||||||
Function / homology | Function and homology information non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / phosphorylation / ATP binding Similarity search - Function | ||||||
Biological species | Rous sarcoma virus | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Holland, D.R. / Rubin, J.R. | ||||||
Citation | Journal: J.Med.Chem. / Year: 1997 Title: Design, synthesis, and cocrystal structure of a nonpeptide Src SH2 domain ligand. Authors: Plummer, M.S. / Holland, D.R. / Shahripour, A. / Lunney, E.A. / Fergus, J.H. / Marks, J.S. / McConnell, P. / Mueller, W.T. / Sawyer, T.K. #1: Journal: Cell(Cambridge,Mass.) / Year: 1993 Title: Binding of a High Affinity Phosphotyrosyl Peptide to the Src Sh2 Domain: Crystal Structures of the Complexed and Peptide-Free Forms Authors: Waksman, G. / Shoelson, S.E. / Pant, N. / Cowburn, D. / Kuriyan, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1skj.cif.gz | 39.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1skj.ent.gz | 30.7 KB | Display | PDB format |
PDBx/mmJSON format | 1skj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sk/1skj ftp://data.pdbj.org/pub/pdb/validation_reports/sk/1skj | HTTPS FTP |
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-Related structure data
Related structure data | 1spsS S: Starting model for refinement |
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Similar 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: 12907.508 Da / Num. of mol.: 1 / Fragment: SH2 DOMAIN / Mutation: N-TERMINAL INS(GS) AND C-TERMINAL INS(EFIVTD) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rous sarcoma virus / Genus: Alpharetrovirus / Strain: SCHMIDT-RUPPIN STRAIN A / Cell line: JM 83 / Cell line (production host): JM83 / Production host: Escherichia coli (E. coli) / References: UniProt: P00524, EC: 2.7.1.112 |
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#2: Chemical | ChemComp-UR2 / |
#3: Water | ChemComp-HOH / |
Sequence details | G-S-A-A-E- - : G-S ARE NOT NATURAL SEQUENCE - BYPRODUCT OF CLONING : E-F-I-V-T-D NOT NATURAL ...G-S-A-A-E- - : G-S ARE NOT NATURAL SEQUENCE - BYPRODUCT OF CLONING : E-F-I-V-T-D NOT NATURAL SEQUENCE - BYPRODUCT OF CLONING |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 48.77 % / Description: WAKSMAN AND KURIYAN SRC SH2 STRUCTURE | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6 Details: 20% PEG 6K, 0.1M ODIUM CACODYLATE PH 6, HANGING DROP EXPERIMENT, PROTEIN 29 MG/ ML, INHIBITOR 4 MG/ML, 4:4:2 RATIO (WELL:PROT:INHIB), pH 6.0, vapor diffusion - hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / pH: 6 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1994 |
Radiation | Monochromator: CU FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→25 Å / Num. obs: 4694 / % possible obs: 95.48 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 7 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PROTEIN MODEL FROM 1SPS Resolution: 2→8 Å / Cross valid method: R-FREE / σ(F): 2.4
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Displacement parameters | Biso mean: 17 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.51 Å / Total num. of bins used: 8
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.2 / Rfactor Rwork: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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