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Yorodumi- PDB-1bkm: COCRYSTAL STRUCTURE OF D-AMINO ACID SUBSTITUTED PHOSPHOPEPTIDE COMPLEX -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bkm | ||||||
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Title | COCRYSTAL STRUCTURE OF D-AMINO ACID SUBSTITUTED PHOSPHOPEPTIDE COMPLEX | ||||||
Components | PP60 V-SRC TYROSINE KINASE TRANSFORMING PROTEIN | ||||||
Keywords | TRANSFORMING PROTEIN / V-SRC SH2 DOMAIN / PHOSPHOTYROSINE RECOGNITION DOMAIN / PP60 SRC SH2 DOMAIN / TRIPEPTIDE / D-AMINO ACID | ||||||
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 / epidermal growth factor receptor signaling pathway / negative regulation of extrinsic apoptotic signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / 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 / epidermal growth factor receptor signaling pathway / negative regulation of extrinsic apoptotic signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / cell adhesion / innate immune response / signaling receptor binding / 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.Am.Chem.Soc. / Year: 1997 Title: Structure-Based Design of a Novel Series of Nonpeptide Ligands that Bind to the Pp60Src Sh2 Domain Authors: Holland, D.R. / Lunney, E.A. / Plummer, M.S. / Mueller, W.T. / Mcconnell, P. / Pavlovsky, A. / Para, K.S. / Shahripour, A. / Humblet, C. / Sawyer, T.K. / Rubin, J.R. #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 | 1bkm.cif.gz | 43.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bkm.ent.gz | 29.4 KB | Display | PDB format |
PDBx/mmJSON format | 1bkm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bkm_validation.pdf.gz | 686.8 KB | Display | wwPDB validaton report |
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Full document | 1bkm_full_validation.pdf.gz | 690.8 KB | Display | |
Data in XML | 1bkm_validation.xml.gz | 5.3 KB | Display | |
Data in CIF | 1bkm_validation.cif.gz | 7.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/1bkm ftp://data.pdbj.org/pub/pdb/validation_reports/bk/1bkm | HTTPS FTP |
-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: 12821.392 Da / Num. of mol.: 1 / Fragment: DOMAIN / Mutation: INS(G0,S1), INS(EFIVTD) AT C-TERMINUS Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rous sarcoma virus / Genus: Alpharetrovirus / Strain: SCHMIDT-RUPPIN STRAIN A / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 / References: UniProt: P00524, EC: 2.7.1.112 |
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#2: Chemical | ChemComp-1C5 / [[ |
#3: Water | ChemComp-HOH / |
Sequence details | 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 Å3/Da / Density % sol: 40.22 % / Description: WAKSMAN AND KURIYAN SRC SH2 STRUCTURE | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 8 Details: 5% PEG 6K, 0.1M TRIS, PH 8, SITTING DROP EXPERIMENT, PROTEIN 50 MG/ML, INHIBITOR 4 MG/ML, 4:4:2 RATIO (WELL:PROT:INHIB), pH 8.0, vapor diffusion - sitting drop | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging dropDetails: 4 micro litter of protein solution was mixed with 2 micro litter of 5 solution and 4 micro litter of reservoir solution | ||||||||||||||||||||||||||||||||||||||||||
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→25 Å / Num. obs: 6768 / % possible obs: 88.7 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2→2.12 Å / Redundancy: 2 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 5 / % possible all: 71.9 |
Reflection shell | *PLUS % possible obs: 71.9 % |
-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
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Displacement parameters | Biso mean: 20.6 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→2.1 Å / Total num. of bins used: 8
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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