+Open data
-Basic information
Entry | Database: PDB / ID: 1kav | ||||||
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Title | Human Tyrosine Phosphatase 1B Complexed with an Inhibitor | ||||||
Components | PROTEIN-TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 1 | ||||||
Keywords | HYDROLASE / PROTEIN-INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information PTK6 Down-Regulation / regulation of hepatocyte growth factor receptor signaling pathway / positive regulation of receptor catabolic process / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / insulin receptor recycling / negative regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of IRE1-mediated unfolded protein response / negative regulation of PERK-mediated unfolded protein response / IRE1-mediated unfolded protein response / regulation of intracellular protein transport ...PTK6 Down-Regulation / regulation of hepatocyte growth factor receptor signaling pathway / positive regulation of receptor catabolic process / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / insulin receptor recycling / negative regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of IRE1-mediated unfolded protein response / negative regulation of PERK-mediated unfolded protein response / IRE1-mediated unfolded protein response / regulation of intracellular protein transport / cytoplasmic side of endoplasmic reticulum membrane / sorting endosome / mitochondrial crista / platelet-derived growth factor receptor-beta signaling pathway / regulation of type I interferon-mediated signaling pathway / regulation of endocytosis / positive regulation of protein tyrosine kinase activity / non-membrane spanning protein tyrosine phosphatase activity / peptidyl-tyrosine dephosphorylation / Regulation of IFNA/IFNB signaling / cellular response to unfolded protein / regulation of signal transduction / growth hormone receptor signaling pathway via JAK-STAT / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of signal transduction / Regulation of IFNG signaling / MECP2 regulates neuronal receptors and channels / Growth hormone receptor signaling / endoplasmic reticulum unfolded protein response / negative regulation of MAP kinase activity / positive regulation of JUN kinase activity / negative regulation of insulin receptor signaling pathway / Insulin receptor recycling / ephrin receptor binding / protein dephosphorylation / Integrin signaling / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / protein phosphatase 2A binding / endosome lumen / insulin receptor binding / Negative regulation of MET activity / negative regulation of ERK1 and ERK2 cascade / receptor tyrosine kinase binding / insulin receptor signaling pathway / actin cytoskeleton organization / early endosome / mitochondrial matrix / cadherin binding / protein kinase binding / enzyme binding / endoplasmic reticulum / protein-containing complex / RNA binding / zinc ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Jia, Z. / Ye, Q. / Dinaut, A.N. / Wang, Q. / Waddleton, D. / Payette, P. / Ramachandran, C. / Kennedy, B. / Hum, G. / Taylor, S.D. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2001 Title: Structure of protein tyrosine phosphatase 1B in complex with inhibitors bearing two phosphotyrosine mimetics. Authors: Jia, Z. / Ye, Q. / Dinaut, A.N. / Wang, Q. / Waddleton, D. / Payette, P. / Ramachandran, C. / Kennedy, B. / Hum, G. / Taylor, S.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kav.cif.gz | 76.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kav.ent.gz | 56.9 KB | Display | PDB format |
PDBx/mmJSON format | 1kav.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kav_validation.pdf.gz | 690.6 KB | Display | wwPDB validaton report |
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Full document | 1kav_full_validation.pdf.gz | 697.8 KB | Display | |
Data in XML | 1kav_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 1kav_validation.cif.gz | 20.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ka/1kav ftp://data.pdbj.org/pub/pdb/validation_reports/ka/1kav | HTTPS FTP |
-Related structure data
Related structure data | 1kakC 2hnpS 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: 34720.566 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P18031, protein-tyrosine-phosphatase |
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#2: Chemical | ChemComp-FEP / [( |
#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: 3.6 Å3/Da / Density % sol: 65.82 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 8000, magnesium acetate, HEPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion / Details: Barford, D., (1994) J. Mol. Biol., 239, 726. / pH: 7.5 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.948 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 15, 1998 |
Radiation | Monochromator: CHESS F1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.948 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→25 Å / Num. all: 21925 / Num. obs: 20176 / % possible obs: 92 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.16 % / Biso Wilson estimate: 36.7 Å2 / Rsym value: 0.039 / Net I/σ(I): 32.2 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 22.15 % / Mean I/σ(I) obs: 7.03 / Num. unique all: 1094 / Rsym value: 0.039 / % possible all: 96.6 |
Reflection | *PLUS Lowest resolution: 50 Å / % possible obs: 92.2 % / Num. measured all: 89257 / Rmerge(I) obs: 0.039 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Native PTP1B Structure (2HNP) Resolution: 2.35→6 Å / Isotropic thermal model: Isotropic / Cross valid method: Throught / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.35→6 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 10 % / Rfactor obs: 0.208 / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.208 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.41 |