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Yorodumi- PDB-3qcm: Human receptor protein tyrosine phosphatase gamma, domain 1, in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qcm | ||||||
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Title | Human receptor protein tyrosine phosphatase gamma, domain 1, in complex with 2-[(3,4-dichlorobenzyl)sulfanyl]-4-{[3-({N-[2-(methylamino)ethyl]glycyl}amino)phenyl]ethynyl}benzoic acid | ||||||
Components | Receptor-type tyrosine-protein phosphatase gamma | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / TYROSINE RECEPTOR PHOSPHATASE / TWISTED MIXED BETA-SHEETS FLANKED BY {ALPHA}-HELICES / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information negative regulation of epithelial cell migration / transmembrane receptor protein tyrosine phosphatase activity / dephosphorylation / cell surface receptor protein tyrosine kinase signaling pathway / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / negative regulation of neuron projection development / extracellular exosome / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Sheriff, S. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2011 Title: Small molecule receptor protein tyrosine phosphatase [gamma](RPTP[gamma]) ligands that inhibit phosphatase activity via perturbation of the tryptophan-proline-aspartate (WPD) loop Authors: Sheriff, S. / Beno, B.R. / Zhai, W. / Kostich, W.A. / McDonnell, P.A. / Kish, K. / Goldfarb, V. / Gao, M. / Kiefer, S.E. / Yanchunas, J. / Huang, Y. / Shi, S. / Zhu, S. / Dzierba, C. / ...Authors: Sheriff, S. / Beno, B.R. / Zhai, W. / Kostich, W.A. / McDonnell, P.A. / Kish, K. / Goldfarb, V. / Gao, M. / Kiefer, S.E. / Yanchunas, J. / Huang, Y. / Shi, S. / Zhu, S. / Dzierba, C. / Bronson, J. / Macor, J.E. / Appiah, K.K. / Westphal, R.S. / O'Connell, J. / Gerritz, S.W. #1: Journal: To be Published Title: Cloning, purification, crystallization and preliminary X-ray analysis of the catalytic domain of human receptor-like protein Tyrosine Phosphatase g in three different crystal forms Authors: Kish, K. / McDonnell, P.A. / Goldfarb, V. / Gao, M. / Metzler, W.J. / Langley, D.R. / Bryson, J.W. / Kiefer, S.E. / Kostich, W.A. / Carpenter, B. / Westphal, R.S. / Sheriff, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qcm.cif.gz | 133.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qcm.ent.gz | 103.4 KB | Display | PDB format |
PDBx/mmJSON format | 3qcm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qcm_validation.pdf.gz | 827 KB | Display | wwPDB validaton report |
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Full document | 3qcm_full_validation.pdf.gz | 836 KB | Display | |
Data in XML | 3qcm_validation.xml.gz | 23.9 KB | Display | |
Data in CIF | 3qcm_validation.cif.gz | 32.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qc/3qcm ftp://data.pdbj.org/pub/pdb/validation_reports/qc/3qcm | HTTPS FTP |
-Related structure data
Related structure data | 3qcbC 3qccC 3qcdSC 3qceC 3qcfC 3qcgC 3qchC 3qciC 3qcjC 3qckC 3qclC 3qcnC C: citing same article (ref.) 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 35735.621 Da / Num. of mol.: 2 / Mutation: V948I, S970T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPG, PTPRG / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P23470, protein-tyrosine-phosphatase #2: Chemical | #3: Chemical | #4: 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: 2.52 Å3/Da / Density % sol: 51.21 % |
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Crystal grow | Temperature: 277 K / pH: 6.7 / Details: pH 6.7, vapor diffusion, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.54 |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 23, 2007 / Details: MICROMAX CONFOCAL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 26953 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 51.1 Å2 / Rmerge(I) obs: 0.028 / Net I/σ(I): 43 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 14.6 / % possible all: 93.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3QCD Resolution: 2.4→40.52 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.905 / Occupancy max: 1 / Occupancy min: 0.5 / SU R Cruickshank DPI: 0.39 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.36 / SU Rfree Blow DPI: 0.24 / SU Rfree Cruickshank DPI: 0.25
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Displacement parameters | Biso mean: 47.07 Å2
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Refine analyze | Luzzati coordinate error obs: 0.31 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→40.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.49 Å / Total num. of bins used: 14
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