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Yorodumi- PDB-5i60: X-RAY CRYSTAL STRUCTURE AT 2.12A RESOLUTION OF HUMAN MITOCHONDRIA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5i60 | ||||||
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Title | X-RAY CRYSTAL STRUCTURE AT 2.12A RESOLUTION OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH A BIARL AMIDE COMPOUND AND AN INTERNAL ALDIMINE LINKED PLP COFACTOR. | ||||||
Components | Branched-chain-amino-acid aminotransferase, mitochondrial | ||||||
Keywords | TRANSFERASE / FOLD TYPE IV | ||||||
Function / homology | Function and homology information 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 / amino acid biosynthetic process / cellular response to leukemia inhibitory factor / lipid metabolic process / mitochondrial matrix / mitochondrion / nucleoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.12 Å | ||||||
Authors | Somers, D.O. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5i60.cif.gz | 170.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5i60.ent.gz | 132.9 KB | Display | PDB format |
PDBx/mmJSON format | 5i60.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5i60_validation.pdf.gz | 972.9 KB | Display | wwPDB validaton report |
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Full document | 5i60_full_validation.pdf.gz | 979.5 KB | Display | |
Data in XML | 5i60_validation.xml.gz | 33.2 KB | Display | |
Data in CIF | 5i60_validation.cif.gz | 48.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i6/5i60 ftp://data.pdbj.org/pub/pdb/validation_reports/i6/5i60 | HTTPS FTP |
-Related structure data
Related structure data | 5i5sC 5i5tC 5i5uC 5i5vC 5i5wC 5i5xC 5i5yC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Homo sapiens (human) / Gene: BCAT2, BCATM, BCT2, ECA40 / Production host: Escherichia coli (E. coli) References: UniProt: O15382, branched-chain-amino-acid transaminase |
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-Non-polymers , 5 types, 506 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.59 % |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 29, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.12→40 Å / Num. obs: 45566 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 33.5 Å2 / Rmerge(I) obs: 0.077 / Net I/av σ(I): 24.202 / Net I/σ(I): 9.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: In-house structure Resolution: 2.12→20 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.257 / SU ML: 0.136 / SU R Cruickshank DPI: 0.209 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.187 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: 113.91 Å2 / Biso mean: 41.319 Å2 / Biso min: 19.1 Å2
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Refinement step | Cycle: final / Resolution: 2.12→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.12→2.174 Å / Total num. of bins used: 20
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