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Yorodumi- PDB-2h02: Structural studies of protein tyrosine phosphatase beta catalytic... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2h02 | ||||||
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Title | Structural studies of protein tyrosine phosphatase beta catalytic domain in complex with inhibitors | ||||||
Components | Protein tyrosine phosphatase, receptor type, B, | ||||||
Keywords | HYDROLASE / protein tyrosine phosphatase / WPD-loop / sulfamic acid / phosphatase / inhibitor / drug design | ||||||
Function / homology | Function and homology information glial cell migration / transmembrane receptor protein tyrosine phosphatase activity / phosphate-containing compound metabolic process / dephosphorylation / tertiary granule membrane / specific granule membrane / protein dephosphorylation / protein-tyrosine-phosphatase / angiogenesis / receptor complex ...glial cell migration / transmembrane receptor protein tyrosine phosphatase activity / phosphate-containing compound metabolic process / dephosphorylation / tertiary granule membrane / specific granule membrane / protein dephosphorylation / protein-tyrosine-phosphatase / angiogenesis / receptor complex / cadherin binding / Neutrophil degranulation / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Evdokimov, A.G. / Pokross, M.E. / Walter, R.L. / Mekel, M. / Gray, J.L. / Peters, K.G. / Maier, M.B. / Amarasinghe, K.D. / Clark, C.M. / Nichols, R. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2006 Title: Design and synthesis of potent, non-peptidic inhibitors of HPTPbeta. Authors: Amarasinghe, K.K. / Evdokimov, A.G. / Xu, K. / Clark, C.M. / Maier, M.B. / Srivastava, A. / Colson, A.O. / Gerwe, G.S. / Stake, G.E. / Howard, B.W. / Pokross, M.E. / Gray, J.L. / Peters, K.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2h02.cif.gz | 136.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h02.ent.gz | 106.8 KB | Display | PDB format |
PDBx/mmJSON format | 2h02.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2h02_validation.pdf.gz | 1015.4 KB | Display | wwPDB validaton report |
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Full document | 2h02_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 2h02_validation.xml.gz | 28.7 KB | Display | |
Data in CIF | 2h02_validation.cif.gz | 39.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h0/2h02 ftp://data.pdbj.org/pub/pdb/validation_reports/h0/2h02 | HTTPS FTP |
-Related structure data
Related structure data | 2h03C 2h04C 1rpmS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 36288.035 Da / Num. of mol.: 2 / Fragment: catalytic domain, residues 1662-1973 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRB / Plasmid: pDEST-HisMBP / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 References: UniProt: Q3MIV7, UniProt: P23467*PLUS, protein-tyrosine-phosphatase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.85 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 8 Details: 21% PEG 8000, 220 mM MgCl2, 1% BME, 0.1% BOG, 5mM DTT, pH 8.0, vapor diffusion, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 1, 2006 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 32002 / Num. obs: 32002 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 31.1 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 15.69 |
Reflection shell | Resolution: 2.15→2.25 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.76 / Num. unique all: 2904 / % possible all: 68.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RPM Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.909 / SU B: 12.085 / SU ML: 0.159 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.402 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.586 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Selection: ALL
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