+Open data
-Basic information
Entry | Database: PDB / ID: 1bzc | ||||||
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Title | HUMAN PTP1B CATALYTIC DOMAIN COMPLEXED WITH TPI | ||||||
Components | PROTEIN (PROTEIN-TYROSINE-PHOSPHATASE) | ||||||
Keywords | HYDROLASE / HYDROLASE(PHOSPHORYLATION) / TYROSINE PHOSPHATASE / 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 / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Groves, M.R. / Yao, Z.J. / Jr Burke, T.R. / Barford, D. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: Structural basis for inhibition of the protein tyrosine phosphatase 1B by phosphotyrosine peptide mimetics. Authors: Groves, M.R. / Yao, Z.J. / Roller, P.P. / Burke Jr., T.R. / Barford, D. #1: Journal: Science / Year: 1994 Title: The Crystal Structure of Human Protein Tyrosine Phosphatase 1B Authors: Barford, D. / Flint, A.J. / Tonks, N.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bzc.cif.gz | 78.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bzc.ent.gz | 57.8 KB | Display | PDB format |
PDBx/mmJSON format | 1bzc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bzc_validation.pdf.gz | 737 KB | Display | wwPDB validaton report |
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Full document | 1bzc_full_validation.pdf.gz | 741.4 KB | Display | |
Data in XML | 1bzc_validation.xml.gz | 15 KB | Display | |
Data in CIF | 1bzc_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bz/1bzc ftp://data.pdbj.org/pub/pdb/validation_reports/bz/1bzc | HTTPS FTP |
-Related structure data
Related structure data | 1bzhC 1bzjC 2hnpS 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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Unit cell |
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-Components
#1: Protein | Mass: 37365.637 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: P18031, protein-tyrosine-phosphatase |
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#2: Chemical | ChemComp-TPI / |
#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: 3.61 Å3/Da / Density % sol: 65.62 % | |||||||||||||||||||||||||
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Crystal grow | pH: 8 / Details: pH 8.0 | |||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion / Details: Barfoed, D., (1994) J. Mol. Biol., 239, 726. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→24 Å / Num. obs: 28772 / % possible obs: 94.4 % / Redundancy: 2.3 % / Biso Wilson estimate: 33.99 Å2 / Rmerge(I) obs: 0.033 / Rsym value: 0.033 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 2.35→2.48 Å / Rmerge(I) obs: 0.089 / Mean I/σ(I) obs: 8.2 / Rsym value: 0.089 / % possible all: 93.8 |
Reflection | *PLUS Num. obs: 18772 / Num. measured all: 65906 |
Reflection shell | *PLUS % possible obs: 93.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2HNP Resolution: 2.35→14 Å / Cross valid method: THROUGHOUT / σ(F): 0 Details: VALUES QUOTED FOR PLANAR RESTRAINTS ARE FOR THE AROMATICS. PEPTIDE VALUES ARE RMS=0.0132, SIGMA=0.03.
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Displacement parameters | Biso mean: 25.98 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→14 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.204 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.35 Å / Lowest resolution: 2.48 Å / Rfactor Rfree: 0.278 / Rfactor obs: 0.253 |