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Yorodumi- PDB-1shb: CRYSTAL STRUCTURE OF THE PHOSPHOTYROSINE RECOGNITION DOMAIN SH2 O... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1shb | ||||||
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Title | CRYSTAL STRUCTURE OF THE PHOSPHOTYROSINE RECOGNITION DOMAIN SH2 OF V-SRC COMPLEXED WITH TYROSINE-PHOSPHORYLATED PEPTIDES | ||||||
Components |
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Keywords | PHOSPHOTRANSFERASE | ||||||
Function / homology | Function and homology information osteoclast development / progesterone receptor signaling pathway / extrinsic component of cytoplasmic side of plasma membrane / bone resorption / negative regulation of intrinsic apoptotic signaling pathway / 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 / extrinsic component of cytoplasmic side of plasma membrane / bone resorption / negative regulation of intrinsic apoptotic signaling pathway / 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 / innate immune response / signaling receptor binding / ATP binding Similarity search - Function | ||||||
Biological species | Rous sarcoma virus | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Waksman, G. / Kuriyan, J. | ||||||
Citation | Journal: Nature / Year: 1992 Title: Crystal structure of the phosphotyrosine recognition domain SH2 of v-src complexed with tyrosine-phosphorylated peptides. Authors: Waksman, G. / Kominos, D. / Robertson, S.C. / Pant, N. / Baltimore, D. / Birge, R.B. / Cowburn, D. / Hanafusa, H. / Mayer, B.J. / Overduin, M. / Resh, M.D. / Rios, C.B. / Silverman, L. / Kuriyan, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1shb.cif.gz | 33.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1shb.ent.gz | 22.9 KB | Display | PDB format |
PDBx/mmJSON format | 1shb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sh/1shb ftp://data.pdbj.org/pub/pdb/validation_reports/sh/1shb | 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: 11970.480 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rous sarcoma virus / Genus: Alpharetrovirus / References: UniProt: P00524, EC: 2.7.1.112 |
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#2: Protein/peptide | Mass: 701.728 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rous sarcoma virus / Genus: Alpharetrovirus |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.42 % | ||||||||||||||||||||
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Crystal grow | *PLUS pH: 8 / Method: vapor diffusion | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2 Å / % possible obs: 91 % / Rmerge(I) obs: 0.067 |
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-Processing
Software |
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Refinement | Resolution: 2→6 Å / Rfactor Rwork: 0.19 / Rfactor obs: 0.19 / σ(F): 2 Details: THE LOOP FROM RESIDUE 49 TO 53 IS DISORDERED AND IS NOT CLEARLY VISIBLE IN THE ELECTRON DENSITY. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→6 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 6 Å / σ(F): 2 / Rfactor obs: 0.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3.1 |