+Open data
-Basic information
Entry | Database: PDB / ID: 1khb | ||||||
---|---|---|---|---|---|---|---|
Title | PEPCK complex with nonhydrolyzable GTP analog, native 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 / glyceraldehyde-3-phosphate biosynthetic process / carboxylic acid binding / 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 / Resolution: 1.854 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 | 1khb.cif.gz | 137.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1khb.ent.gz | 104.2 KB | Display | PDB format |
PDBx/mmJSON format | 1khb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kh/1khb ftp://data.pdbj.org/pub/pdb/validation_reports/kh/1khb | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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) |
---|
-Non-polymers , 5 types, 238 molecules
#2: Chemical | #3: Chemical | ChemComp-ACT / | #4: Chemical | ChemComp-GCP / | #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.96 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 pH: 7.5 / 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: 1.072 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 |
Reflection | Resolution: 1.854→20 Å / Num. obs: 47525 / % possible obs: 94.7 % / Rsym value: 0.027 |
Reflection | *PLUS Rmerge(I) obs: 0.027 |
-Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.854→20 Å / SU B: 1.69009 / SU ML: 0.05201 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15395 / ESU R Free: 0.14197
| ||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.902 Å2
| ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.854→20 Å
| ||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||
Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS |