+Open data
-Basic information
Entry | Database: PDB / ID: 1khe | ||||||
---|---|---|---|---|---|---|---|
Title | PEPCK complex with nonhydrolyzable GTP analog, MAD data | ||||||
Components | Phosphoenolpyruvate Carboxykinase, cytosolic (GTP) | ||||||
Keywords | LYASE / Gluconeogenesis / P-loop | ||||||
Function / homology | Function and homology information cellular response to potassium ion starvation / protein serine kinase activity (using GTP as donor) / Abacavir metabolism / response to methionine / glycerol biosynthetic process from pyruvate / Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases / phosphoenolpyruvate carboxykinase (GTP) / phosphoenolpyruvate carboxykinase (GTP) activity / propionate catabolic process / cellular response to raffinose ...cellular response to potassium ion starvation / protein serine kinase activity (using GTP as donor) / Abacavir metabolism / response to methionine / glycerol biosynthetic process from pyruvate / Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases / 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 / cellular hypotonic salinity response / carboxylic acid binding / glyceraldehyde-3-phosphate biosynthetic process / cellular response to phorbol 13-acetate 12-myristate / oxaloacetate metabolic process / hepatocyte differentiation / positive regulation of memory T cell differentiation / Gluconeogenesis / cellular hyperosmotic salinity response / response to starvation / cellular response to glucagon stimulus / positive regulation of lipid biosynthetic process / cellular response to interleukin-1 / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / 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 / GDP binding / glucose metabolic process / glucose homeostasis / cellular response to tumor necrosis factor / 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 / SYNCHROTRON / MAD / Resolution: 2.4 Å | ||||||
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. | ||||||
Citation | 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1khe.cif.gz | 132.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1khe.ent.gz | 107.4 KB | Display | PDB format |
PDBx/mmJSON format | 1khe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kh/1khe ftp://data.pdbj.org/pub/pdb/validation_reports/kh/1khe | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 70561.406 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) | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-GCP / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.87 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG1500, MES, DTT, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 110 K | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.971270, 0.978947, 0.978838 | ||||||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 19, 1998 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
| ||||||||||||
Reflection | Resolution: 2.4→20 Å / Num. obs: 22522 / % possible obs: 97.9 % / Rsym value: 0.02 | ||||||||||||
Reflection | *PLUS Rmerge(I) obs: 0.02 |
-Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.4→20 Å / SU B: 4.29922 / SU ML: 0.10319 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.69313 / ESU R Free: 0.28921 / Details: High-energy remote data used for refinement
| ||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.409 Å2
| ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
| ||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||
Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS |