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- PDB-7nya: CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC BRANCHED-CHAIN AMINOTRANSFER... -

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Entry
Database: PDB / ID: 7nya
TitleCRYSTAL STRUCTURE OF HUMAN CYTOSOLIC BRANCHED-CHAIN AMINOTRANSFERASE (BCAT1) IN COMPLEX WITH PLP AND SMALL MOLECULE INHIBITOR BAY-069 (COMPOUND 36)
ComponentsBranched-chain-amino-acid aminotransferase, cytosolic
KeywordsTRANSFERASE / BRANCHED-CHAIN-AMINO-ACID AMINOTRANSFERASE / PYRIDOXAL-PHOSPHATE-DEPENDENT AMINOTRANSFERASE / SMALL MOLECULE INHIBITOR
Function / homology
Function and homology information


branched-chain-amino-acid transaminase activity / branched-chain amino acid biosynthetic process / L-leucine-2-oxoglutarate transaminase activity / branched-chain-amino-acid transaminase / : / L-valine-2-oxoglutarate transaminase activity / L-isoleucine-2-oxoglutarate transaminase activity / Branched-chain amino acid catabolism / L-leucine biosynthetic process / L-valine biosynthetic process ...branched-chain-amino-acid transaminase activity / branched-chain amino acid biosynthetic process / L-leucine-2-oxoglutarate transaminase activity / branched-chain-amino-acid transaminase / : / L-valine-2-oxoglutarate transaminase activity / L-isoleucine-2-oxoglutarate transaminase activity / Branched-chain amino acid catabolism / L-leucine biosynthetic process / L-valine biosynthetic process / lipid metabolic process / G1/S transition of mitotic cell cycle / mitochondrion / cytosol
Similarity search - Function
Branched-chain amino acid aminotransferase II / Branched-chain aminotransferase / Aminotransferase, class IV, conserved site / Aminotransferases class-IV signature. / Branched-chain-amino-acid aminotransferase-like, N-terminal / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, C-terminal / Amino-transferase class IV
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Chem-UUZ / Branched-chain-amino-acid aminotransferase, cytosolic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsHillig, R.C.
CitationJournal: J.Med.Chem. / Year: 2022
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
DepositionMar 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Branched-chain-amino-acid aminotransferase, cytosolic
B: Branched-chain-amino-acid aminotransferase, cytosolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,7707
Polymers86,5812
Non-polymers1,1895
Water10,287571
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-43 kcal/mol
Surface area26870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.584, 103.294, 108.118
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

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

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Branched-chain-amino-acid aminotransferase, cytosolic / BCAT(c) / Protein ECA39 / BCAT1


Mass: 43290.312 Da / Num. of mol.: 2 / Mutation: Ser379Arg, engineered
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCAT1, BCT1, ECA39 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P54687, branched-chain-amino-acid transaminase
#2: Chemical ChemComp-UUZ / 3-[4-chloranyl-3-(2-methylphenoxy)naphthalen-1-yl]-6-(trifluoromethyl)-5~{H}-pyrimidine-2,4-dione


Mass: 446.806 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H14ClF3N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 571 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.71 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSVERSION Jan 26, 2018data reduction
PHASERphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
pointlessversion 1.11.17data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ABJ

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.
RfactorNum. reflection% reflectionSelection details
Rfree0.2213 2101 3.3 %RANDOM
Rwork0.1827 ---
obs0.184 62095 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 123.16 Å2 / Biso mean: 28.119 Å2 / Biso min: 15.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20 Å2
2---0.1 Å20 Å2
3----0.2 Å2
Refinement stepCycle: final / Resolution: 1.85→47.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5754 0 79 572 6405
Biso mean--35.46 35.88 -
Num. residues----727
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0136078
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175674
X-RAY DIFFRACTIONr_angle_refined_deg1.361.6628295
X-RAY DIFFRACTIONr_angle_other_deg1.2461.57913086
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9065749
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.07422.691301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.096151017
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5481533
X-RAY DIFFRACTIONr_chiral_restr0.0590.2770
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026846
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021363
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

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 152 -
Rwork0.323 4469 -
all-4621 -
obs--98.78 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6241-0.1587-0.3560.43090.25530.72820.01990.00520.08550.0046-0.0034-0.0849-0.05180.1467-0.01650.0054-0.0129-0.00890.12560.02310.20983.6757.056-17.333
20.67880.38130.35330.53940.48540.80080.0152-0.0331-0.00960.0523-0.04050.05440.0519-0.08620.02540.00680.00060.0150.11950.01440.1671-22.047-11.495-4.352
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 386
2X-RAY DIFFRACTION2B24 - 386

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