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- PDB-2f5z: Crystal Structure of Human Dihydrolipoamide Dehydrogenase (E3) Co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2f5z | ||||||
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Title | Crystal Structure of Human Dihydrolipoamide Dehydrogenase (E3) Complexed to the E3-Binding Domain of Human E3-Binding Protein | ||||||
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![]() | OXIDOREDUCTASE/PROTEIN BINDING / protein-protein complex / OXIDOREDUCTASE-PROTEIN BINDING COMPLEX | ||||||
Function / homology | ![]() acetyltransferase complex / acrosomal matrix / Glycine degradation / : / dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase activity / acetyl-CoA biosynthetic process from pyruvate / Lysine catabolism / oxoglutarate dehydrogenase complex / : ...acetyltransferase complex / acrosomal matrix / Glycine degradation / : / dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase activity / acetyl-CoA biosynthetic process from pyruvate / Lysine catabolism / oxoglutarate dehydrogenase complex / : / branched-chain amino acid catabolic process / Citric acid cycle (TCA cycle) / pyruvate dehydrogenase complex / Branched-chain amino acid catabolism / Pyruvate metabolism / Glyoxylate metabolism and glycine degradation / Regulation of pyruvate dehydrogenase (PDH) complex / motile cilium / sperm capacitation / Signaling by Retinoic Acid / acyltransferase activity / mitochondrial electron transport, NADH to ubiquinone / gastrulation / Mitochondrial protein degradation / regulation of membrane potential / flavin adenine dinucleotide binding / mitochondrial matrix / mitochondrion / proteolysis / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Brautigam, C.A. / Chuang, J.L. / Wynn, R.M. / Tomchick, D.R. / Machius, M. / Chuang, D.T. | ||||||
![]() | ![]() Title: Structural Insight into Interactions between Dihydrolipoamide Dehydrogenase (E3) and E3 Binding Protein of Human Pyruvate Dehydrogenase Complex. Authors: Brautigam, C.A. / Wynn, R.M. / Chuang, J.L. / Machius, M. / Tomchick, D.R. / Chuang, D.T. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1, 2, 3, 4, 5 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS ...BIOMOLECULE: 1, 2, 3, 4, 5 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 15CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). AUTHORS INDICATE THAT BIOMOLECULE 1 BEST REPRESENTS THE PHYSIOLOGICAL COMPLEX |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 977.8 KB | Display | ![]() |
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PDB format | ![]() | 807.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.8 MB | Display | ![]() |
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Full document | ![]() | 2.9 MB | Display | |
Data in XML | ![]() | 193.3 KB | Display | |
Data in CIF | ![]() | 267.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2f60C ![]() 1zmdS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 50208.406 Da / Num. of mol.: 10 / Fragment: Dihydrolipoyl dehydrogenase, residues 36-509 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 7150.151 Da / Num. of mol.: 5 / Fragment: E3-binding domain, residues 173-230 / Mutation: K120G,T176L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-FAD / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.35 Å3/Da / Density % sol: 63.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 14% (w/v) PEG4000, 0.2 M ammonium sulfate, 0.1 M sodium acetate, 0.03 M spermidine, 8% (v/v) glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Jul 9, 2004 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979426 Å / Relative weight: 1 |
Reflection | Resolution: 2.18→37.4 Å / Num. all: 367237 / Num. obs: 367237 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 31.9 Å2 / Rsym value: 0.054 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 2.18→2.26 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 31492 / Rsym value: 0.401 / % possible all: 84.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1ZMD without NADH Resolution: 2.18→37.4 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Residues of E3BD with missing atoms were modeled as alanine due to missing density for the side chain
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Displacement parameters | Biso mean: 42.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.18→37.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.18→2.32 Å / Rfactor Rfree error: 0.012
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