+Open data
-Basic information
Entry | Database: PDB / ID: 2pnr | ||||||
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Title | Crystal Structure of the asymmetric Pdk3-l2 Complex | ||||||
Components |
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Keywords | TRANSFERASE / pyruvate dehydrogenase kinase 3 / lipoyl-bearing domain / asymmetric protein-protein complex | ||||||
Function / homology | Function and homology information hypoxia-inducible factor-1alpha signaling pathway / [pyruvate dehydrogenase (acetyl-transferring)] kinase / regulation of acetyl-CoA biosynthetic process from pyruvate / pyruvate dehydrogenase (acetyl-transferring) kinase activity / dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / acetyl-CoA biosynthetic process from pyruvate / : / pyruvate dehydrogenase complex / Pyruvate metabolism ...hypoxia-inducible factor-1alpha signaling pathway / [pyruvate dehydrogenase (acetyl-transferring)] kinase / regulation of acetyl-CoA biosynthetic process from pyruvate / pyruvate dehydrogenase (acetyl-transferring) kinase activity / dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / acetyl-CoA biosynthetic process from pyruvate / : / pyruvate dehydrogenase complex / Pyruvate metabolism / Glyoxylate metabolism and glycine degradation / Regulation of pyruvate dehydrogenase (PDH) complex / regulation of reactive oxygen species metabolic process / cellular response to fatty acid / Signaling by Retinoic Acid / regulation of glucose metabolic process / tricarboxylic acid cycle / peroxisome proliferator activated receptor signaling pathway / cellular response to glucose stimulus / glucose metabolic process / peptidyl-serine phosphorylation / protein kinase activity / mitochondrial matrix / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / nucleolus / mitochondrion / ATP binding / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Vassylyev, D.G. / Steussy, C.N. / Devedjiev, Y. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Crystal Structure of an Asymmetric complex of Pyruvate Dehydrogenase Kinase 3 with Lipoyl domain 2 and its Biological Implications Authors: Devedjiev, Y. / Steussy, C.N. / Vassylyev, D.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pnr.cif.gz | 342.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pnr.ent.gz | 275.7 KB | Display | PDB format |
PDBx/mmJSON format | 2pnr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2pnr_validation.pdf.gz | 516.4 KB | Display | wwPDB validaton report |
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Full document | 2pnr_full_validation.pdf.gz | 574.7 KB | Display | |
Data in XML | 2pnr_validation.xml.gz | 70.3 KB | Display | |
Data in CIF | 2pnr_validation.cif.gz | 98 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pn/2pnr ftp://data.pdbj.org/pub/pdb/validation_reports/pn/2pnr | HTTPS FTP |
-Related structure data
Related structure data | 1y8nS 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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2 |
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Unit cell |
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-Components
#1: Protein | [ Mass: 48290.980 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDK3 / Plasmid: PTRCHISB / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: Q15120, [pyruvate dehydrogenase (acetyl-transferring)] kinase #2: Protein | Mass: 14192.097 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DLAT, DLTA / Plasmid: PTRCHISB / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: P10515, dihydrolipoyllysine-residue acetyltransferase #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.1 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 Details: Protein solution: 5mg/ml, 20mM Tris-HCL pH 8.0, 100mM NaCl, 5mM DTT, 2.5% (v/v) ethylen glycol Precipitant solution: 100mM histidine, 30 mM EDTA, 7% (v/v) MPD., VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 18, 2002 |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. all: 64645 / Num. obs: 64645 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 41 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 1.5 / Num. unique all: 4439 / Rsym value: 0.422 / % possible all: 64 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Y8N Resolution: 2.5→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: THE PERFECT MEROHEDRAL TWINNING WAS DETECTED IN THE CRYSTALS WITH THE TWINNING OPERATOR {H,-K,-L}. THE REFINEMENT STATISTICS PRESENTED FOR THIS ENTRY CORRESPONDS TO THE REFINEMENT CARRIED ...Details: THE PERFECT MEROHEDRAL TWINNING WAS DETECTED IN THE CRYSTALS WITH THE TWINNING OPERATOR {H,-K,-L}. THE REFINEMENT STATISTICS PRESENTED FOR THIS ENTRY CORRESPONDS TO THE REFINEMENT CARRIED OUT USING THE TWINNING OPTION OF THE CNS PROGRAM. FOR THE DEPOSITION THE DIFFRACTION DATA WERE DETWINNED USING THE CNS PROGRAM. THE REFINEMENT STATISTICS CALCULATED BASED ON THE DETWINNED DATA MIGHT BE SLIGHTLY DIFFERENT FROM THOSE OBTAINED DURING THE "TWINNED" REFINEMENT INCLUDED IN THIS ENTRY.
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.59 Å
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