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- PDB-7nya: CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC BRANCHED-CHAIN AMINOTRANSFER... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7nya | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC BRANCHED-CHAIN AMINOTRANSFERASE (BCAT1) IN COMPLEX WITH PLP AND SMALL MOLECULE INHIBITOR BAY-069 (COMPOUND 36) | ||||||
![]() | Branched-chain-amino-acid aminotransferase, cytosolic | ||||||
![]() | TRANSFERASE / BRANCHED-CHAIN-AMINO-ACID AMINOTRANSFERASE / PYRIDOXAL-PHOSPHATE-DEPENDENT AMINOTRANSFERASE / SMALL MOLECULE INHIBITOR | ||||||
Function / homology | ![]() 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 ...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 / lipid metabolic process / G1/S transition of mitotic cell cycle / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Hillig, R.C. | ||||||
![]() | ![]() Title: BAY-069, a Novel (Trifluoromethyl)pyrimidinedione-Based BCAT1/2 Inhibitor and Chemical Probe. Authors: Gunther, J. / Hillig, R.C. / Zimmermann, K. / Kaulfuss, S. / Lemos, C. / Nguyen, D. / Rehwinkel, H. / Habgood, M. / Lechner, C. / Neuhaus, R. / Ganzer, U. / Drewes, M. / Chai, J. / Bouche, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 312.2 KB | Display | ![]() |
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PDB format | ![]() | 251 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7ntrC ![]() 7nwaC ![]() 7nwbC ![]() 7nwcC ![]() 7nweC ![]() 7nwmC ![]() 7nxnC ![]() 7nxoC ![]() 7ny2C ![]() 7ny9C ![]() 2abjS C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 24 - 385 / Label seq-ID: 27 - 388
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Components
#1: Protein | Mass: 43290.312 Da / Num. of mol.: 2 / Mutation: Ser379Arg, engineered Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P54687, branched-chain-amino-acid transaminase #2: Chemical | #3: Chemical | ChemComp-PLP / | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PROTEIN AT 17 MG/ML IN 10 MILLIMOLAR TRIS-HCL PH 8.0, 100 MILLIMOLAR NACL, 3 MILLIMOLAR DTT. PROTEIN PREINCUBATED OVER NIGHT AT 293 K WITH 10 MILLIMOLAR 3-PHENYL-PROPIONATE, 3 MILLIMOLAR DTT ...Details: PROTEIN AT 17 MG/ML IN 10 MILLIMOLAR TRIS-HCL PH 8.0, 100 MILLIMOLAR NACL, 3 MILLIMOLAR DTT. PROTEIN PREINCUBATED OVER NIGHT AT 293 K WITH 10 MILLIMOLAR 3-PHENYL-PROPIONATE, 3 MILLIMOLAR DTT AND 1.5 MILLIMOLAR PLP. DROPS MADE FROM 1 MICROLITER PROTEIN AND 1 MICROLITER RESERVOIR (225 MILLIMOLAR MGCL2, 16-20 % (W/V) PEG 3350). INHIBITOR SOAKED INTO PREFORMED CRYSTALS FOR 1 DAY AT 10 MILLIMOLAR. CRYO: RESERVOIR SOLUTION COMPLEMENTED WITH 20 % (V/V) GLYCEROL AND 10 MILLIMOLAR INHIBITOR |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→47.9 Å / Num. obs: 64223 / % possible obs: 99.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 31.1 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.151 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 1.85→1.96 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 10194 / CC1/2: 0.633 / Rrim(I) all: 1.46 / % possible all: 99.4 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2ABJ Resolution: 1.85→47.9 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU B: 8.369 / SU ML: 0.123 / SU R Cruickshank DPI: 0.1448 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: WITH TLS ADDED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 123.16 Å2 / Biso mean: 28.119 Å2 / Biso min: 15.55 Å2
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Refinement step | Cycle: final / Resolution: 1.85→47.9 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 11342 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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