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Open data
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Basic information
Entry | Database: PDB / ID: 1skj | ||||||
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Title | COCRYSTAL STRUCTURE OF UREA-SUBSTITUTED PHOSPHOPEPTIDE COMPLEX | ||||||
![]() | PP60 V-SRC TYROSINE KINASE TRANSFORMING PROTEIN | ||||||
![]() | TYROSINE-PROTEIN KINASE / V-SRC SH2 DOMAIN / PHOSPHOTYROSINE RECOGNITION DOMAIN / PP60 SRC SH2 DOMAIN / PEPTIDOMIMETIC / UREIDO | ||||||
Function / homology | ![]() osteoclast development / progesterone receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / bone resorption / extrinsic component of cytoplasmic side of plasma membrane / negative regulation of extrinsic apoptotic signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / cell adhesion ...osteoclast development / progesterone receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / bone resorption / extrinsic component of cytoplasmic side of plasma membrane / negative regulation of extrinsic apoptotic signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / cell adhesion / phosphorylation / innate immune response / signaling receptor binding / ATP binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Holland, D.R. / Rubin, J.R. | ||||||
![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 43.9 KB | Display | ![]() |
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PDB format | ![]() | 30.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 722 KB | Display | ![]() |
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Full document | ![]() | 722.7 KB | Display | |
Data in XML | ![]() | 7.6 KB | Display | |
Data in CIF | ![]() | 9.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1spsS S: Starting model for refinement |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() |
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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: ![]() |
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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: ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.2 / Rfactor Rwork: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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