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- PDB-3qcj: Human receptor protein tyrosine phosphatase gamma, domain 1, in c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3qcj | ||||||
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Title | Human receptor protein tyrosine phosphatase gamma, domain 1, in complex with 5-[({3-[(3,4-dichlorobenzyl)sulfanyl]thiophen-2-yl}carbonyl)sulfamoyl]-2-methoxybenzoic acid | ||||||
![]() | Receptor-type tyrosine-protein phosphatase gamma | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / TYROSINE RECEPTOR PHOSPHATASE / TWISTED MIXED BETA-SHEETS FLANKED BY {ALPHA}-HELICES / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | ![]() negative regulation of epithelial cell migration / transmembrane receptor protein tyrosine phosphatase activity / 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Sheriff, S. | ||||||
![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.7 KB | Display | ![]() |
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PDB format | ![]() | 54.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3qcbC ![]() 3qccC ![]() 3qcdSC ![]() 3qceC ![]() 3qcfC ![]() 3qcgC ![]() 3qchC ![]() 3qciC ![]() 3qckC ![]() 3qclC ![]() 3qcmC ![]() 3qcnC C: citing same article ( 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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Unit cell |
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Components
#1: Protein | Mass: 35707.570 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-NX4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.53 Å3/Da / Density % sol: 65.11 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 7 / Details: pH 7.0, vapor diffusion, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 30, 2006 / Details: VARIMAX HR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→50 Å / Num. obs: 23970 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 8.9 % / Biso Wilson estimate: 37.7 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.26→2.34 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 5.4 / % possible all: 96.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3QCD Resolution: 2.26→40.12 Å / Rfactor Rfree error: 0.009 / Occupancy max: 1 / Occupancy min: 0 / Data cutoff high absF: 1440528 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.8359 Å2 / ksol: 0.3267 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 92.46 Å2 / Biso mean: 46.2816 Å2 / Biso min: 23.34 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.26→40.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.26→2.36 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 8
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Xplor file |
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