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- PDB-5i5w: X-RAY CRYSTAL STRUCTURE AT 2.40A RESOLUTION OF HUMAN MITOCHONDRIA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5i5w | ||||||
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Title | X-RAY CRYSTAL STRUCTURE AT 2.40A RESOLUTION OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH A BIARYL AMIDE COMPOUND AND AN INTERNAL ALDIMINE LINKED PLP COFACTOR. | ||||||
![]() | Branched-chain-amino-acid aminotransferase, mitochondrial | ||||||
![]() | TRANSFERASE / FOLD TYPE IV | ||||||
Function / homology | ![]() regulation of hormone levels / isoleucine catabolic process / L-leucine:2-oxoglutarate aminotransferase activity / branched-chain-amino-acid transaminase / L-leucine transaminase activity / L-valine transaminase activity / L-isoleucine transaminase activity / branched-chain amino acid biosynthetic process / branched-chain-amino-acid transaminase activity / Branched-chain amino acid catabolism ...regulation of hormone levels / isoleucine catabolic process / L-leucine:2-oxoglutarate aminotransferase activity / branched-chain-amino-acid transaminase / L-leucine transaminase activity / L-valine transaminase activity / L-isoleucine transaminase activity / branched-chain amino acid biosynthetic process / branched-chain-amino-acid transaminase activity / Branched-chain amino acid catabolism / L-leucine biosynthetic process / valine biosynthetic process / cellular response to leukemia inhibitory factor / lipid metabolic process / mitochondrial matrix / mitochondrion / nucleoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Somers, D.O. | ||||||
![]() | ![]() Title: Structurally Diverse Mitochondrial Branched Chain Aminotransferase (BCATm) Leads with Varying Binding Modes Identified by Fragment Screening. Authors: Borthwick, J.A. / Ancellin, N. / Bertrand, S.M. / Bingham, R.P. / Carter, P.S. / Chung, C.W. / Churcher, I. / Dodic, N. / Fournier, C. / Francis, P.L. / Hobbs, A. / Jamieson, C. / Pickett, S. ...Authors: Borthwick, J.A. / Ancellin, N. / Bertrand, S.M. / Bingham, R.P. / Carter, P.S. / Chung, C.W. / Churcher, I. / Dodic, N. / Fournier, C. / Francis, P.L. / Hobbs, A. / Jamieson, C. / Pickett, S.D. / Smith, S.E. / Somers, D.O. / Spitzfaden, C. / Suckling, C.J. / Young, R.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 170.8 KB | Display | ![]() |
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PDB format | ![]() | 133.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5i5sC ![]() 5i5tC ![]() 5i5uC ![]() 5i5vC ![]() 5i5xC ![]() 5i5yC ![]() 5i60C 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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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 41725.391 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O15382, branched-chain-amino-acid transaminase |
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-Non-polymers , 6 types, 579 molecules ![](data/chem/img/68B.gif)
![](data/chem/img/PLP.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PLP.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: MDL MORPHEUS SCREEN CONDITION B2, DTT |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Aug 30, 2010 / Details: VARIMAX HF | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→75.404 Å / Num. obs: 30622 / % possible obs: 97.8 % / Redundancy: 4.9 % / Biso Wilson estimate: 41.3 Å2 / Rmerge(I) obs: 0.112 / Net I/av σ(I): 6.046 / Net I/σ(I): 11 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: In-house structure Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.903 / SU B: 8.833 / SU ML: 0.205 / SU R Cruickshank DPI: 0.5845 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.584 / ESU R Free: 0.289 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 107.97 Å2 / Biso mean: 33.59 Å2 / Biso min: 11.16 Å2
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Refinement step | Cycle: final / Resolution: 2.4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.461 Å / Total num. of bins used: 20
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