+Open data
-Basic information
Entry | Database: PDB / ID: 1m51 | ||||||
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Title | PEPCK complex with a GTP-competitive inhibitor | ||||||
Components | phosphoenolpyruvate carboxykinase, cytosolic | ||||||
Keywords | LYASE / gluconeogenesis / xanthine / inhibitor | ||||||
Function / homology | Function and homology information protein serine kinase activity (using GTP as donor) / Abacavir metabolism / cellular response to potassium ion starvation / response to methionine / Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases / glycerol biosynthetic process from pyruvate / phosphoenolpyruvate carboxykinase (GTP) / phosphoenolpyruvate carboxykinase (GTP) activity / propionate catabolic process / cellular response to raffinose ...protein serine kinase activity (using GTP as donor) / Abacavir metabolism / cellular response to potassium ion starvation / response to methionine / Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases / glycerol biosynthetic process from pyruvate / phosphoenolpyruvate carboxykinase (GTP) / phosphoenolpyruvate carboxykinase (GTP) activity / propionate catabolic process / cellular response to raffinose / tricarboxylic acid metabolic process / regulation of lipid biosynthetic process / response to interleukin-6 / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / cellular response to fructose stimulus / carboxylic acid binding / cellular hypotonic salinity response / cellular response to phorbol 13-acetate 12-myristate / oxaloacetate metabolic process / hepatocyte differentiation / positive regulation of memory T cell differentiation / Gluconeogenesis / glyceraldehyde-3-phosphate biosynthetic process / cellular hyperosmotic salinity response / cellular response to glucagon stimulus / response to starvation / cellular response to interleukin-1 / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of lipid biosynthetic process / cellular response to retinoic acid / cellular response to cAMP / cellular response to dexamethasone stimulus / response to activity / gluconeogenesis / cellular response to glucose stimulus / response to insulin / Transcriptional regulation of white adipocyte differentiation / cellular response to insulin stimulus / glucose metabolic process / GDP binding / cellular response to tumor necrosis factor / glucose homeostasis / manganese ion binding / cellular response to hypoxia / peptidyl-serine phosphorylation / response to lipopolysaccharide / GTP binding / magnesium ion binding / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / extracellular exosome / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / rigid-body refinement / Resolution: 2.25 Å | ||||||
Authors | Foley, L.H. / Wang, P. / Dunten, P. / Wertheimer, S.J. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2003 Title: X-ray Structures of two xanthine inhibitors bound to PEPCK and N-3 modifications of substituted 1,8-Dibenzylxanthines Authors: Foley, L.H. / Wang, P. / Dunten, P. / Ramsey, G. / Gubler, M.-L. / Wertheimer, S.J. #1: Journal: J.Mol.Biol. / Year: 2002 Title: Crystal Structure of Human Cytosolic Phosphoenolpyruvate Carboxykinase Reveals a New GTP-Binding Site Authors: Dunten, P. / Belunis, C. / Crowther, R. / Hollfelder, K. / Kammlott, U. / Levin, W. / Michel, H. / Ramsey, G.B. / Swain, A. / Weber, D. / Wertheimer, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m51.cif.gz | 135.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m51.ent.gz | 103.5 KB | Display | PDB format |
PDBx/mmJSON format | 1m51.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m5/1m51 ftp://data.pdbj.org/pub/pdb/validation_reports/m5/1m51 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 69529.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PCK1 / Production host: Escherichia coli (E. coli) References: UniProt: P35558, phosphoenolpyruvate carboxykinase (GTP) |
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-Non-polymers , 5 types, 188 molecules
#2: Chemical | ChemComp-MN / | ||
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#3: Chemical | ChemComp-ACT / | ||
#4: Chemical | ChemComp-TSX / | ||
#5: Chemical | #6: 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: 2.21 Å3/Da / Density % sol: 44.34 % |
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Crystal grow | Method: vapor diffusion / Details: VAPOR DIFFUSION |
Crystal grow | *PLUS Method: unknown |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 29, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→30 Å / Num. obs: 26567 / % possible obs: 94.1 % / Redundancy: 1.9 % / Rsym value: 0.044 / Net I/σ(I): 29.6 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 1.7 % / Rsym value: 0.06 / % possible all: 88.2 |
-Processing
Software |
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Refinement | Method to determine structure: rigid-body refinement / Resolution: 2.25→50 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.896 / SU B: 5.998 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.396 / ESU R Free: 0.396
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.051 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.309 Å / Total num. of bins used: 20
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Refinement | *PLUS Rfactor Rwork: 0.181 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |