+Open data
-Basic information
Entry | Database: PDB / ID: 5kqm | ||||||
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Title | Co-crystal structure of LMW-PTP in complex with MES | ||||||
Components | Low molecular weight phosphotyrosine protein phosphatase | ||||||
Keywords | HYDROLASE / LMW-PTP / Inhibitor / Complex | ||||||
Function / homology | Function and homology information acid phosphatase / acid phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / sarcolemma / cytoplasmic side of plasma membrane / extracellular exosome / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å | ||||||
Authors | Wang, J. / Zhang, Z.-Y. / Yu, Z.-H. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2016 Title: Inhibition of low molecular weight protein tyrosine phosphatase by an induced-fit mechanism. Authors: He, R. / Wang, J. / Yu, Z.H. / Zhang, R.Y. / Liu, S. / Wu, L. / Zhang, Z.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kqm.cif.gz | 48.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kqm.ent.gz | 31.9 KB | Display | PDB format |
PDBx/mmJSON format | 5kqm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kqm_validation.pdf.gz | 440.4 KB | Display | wwPDB validaton report |
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Full document | 5kqm_full_validation.pdf.gz | 440.5 KB | Display | |
Data in XML | 5kqm_validation.xml.gz | 9.4 KB | Display | |
Data in CIF | 5kqm_validation.cif.gz | 12.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kq/5kqm ftp://data.pdbj.org/pub/pdb/validation_reports/kq/5kqm | HTTPS FTP |
-Related structure data
Related structure data | 5kqgC 5kqlC 5kqpC 5pntS 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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Unit cell |
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-Components
#1: Protein | Mass: 20236.879 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACP1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P24666, protein-tyrosine-phosphatase, acid phosphatase |
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#2: Chemical | ChemComp-MES / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30% PEGME 5000, 0.2 M ammonium sulfate, 100 mM MES, pH=6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 2, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→50 Å / Num. obs: 14276 / % possible obs: 99.7 % / Redundancy: 6.6 % / Net I/σ(I): 27.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5PNT Resolution: 1.91→27.463 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.02
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Bsol: 35.385 Å2 / ksol: 0.36 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.91→27.463 Å
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Refine LS restraints |
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LS refinement shell |
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