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- PDB-2xh1: Crystal structure of human KAT II-inhibitor complex -

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Basic information

Entry
Database: PDB / ID: 2xh1
TitleCrystal structure of human KAT II-inhibitor complex
ComponentsKYNURENINE/ALPHA-AMINOADIPATE AMINOTRANSFERASE, MITOCHONDRIAL
KeywordsTRANSFERASE / COVALENT INHIBITION
Function / homology
Function and homology information


glycine transaminase / methionine-glyoxylate transaminase / glycine:2-oxoglutarate aminotransferase activity / methionine-glyoxylate transaminase activity / 2-aminoadipate transaminase / alpha-amino acid metabolic process / 2-aminoadipate transaminase activity / kynurenine-glyoxylate transaminase activity / kynurenine-glyoxylate transaminase / L-lysine catabolic process to acetyl-CoA via saccharopine ...glycine transaminase / methionine-glyoxylate transaminase / glycine:2-oxoglutarate aminotransferase activity / methionine-glyoxylate transaminase activity / 2-aminoadipate transaminase / alpha-amino acid metabolic process / 2-aminoadipate transaminase activity / kynurenine-glyoxylate transaminase activity / kynurenine-glyoxylate transaminase / L-lysine catabolic process to acetyl-CoA via saccharopine / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / kynurenine metabolic process / glutamate metabolic process / Lysine catabolism / 2-oxoglutarate metabolic process / Tryptophan catabolism / biosynthetic process / pyridoxal phosphate binding / mitochondrial matrix / protein homodimerization activity
Similarity search - Function
Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-BF5 / IODIDE ION / PYRIDOXAL-5'-PHOSPHATE / Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRossi, F. / Casazza, V. / Garavaglia, S. / Sathyasaikumar, K.V. / Schwarcz, R. / Kojima, S.I. / Okuwaki, K. / Ono, S.I. / Kajii, Y. / Rizzi, M.
CitationJournal: J.Med.Chem. / Year: 2010
Title: Crystal Structure-Based Selective Targeting of the Pyridoxal 5'-Phsosphate Dependent Enzyme Kynurenine Aminotransferase II for Cognitive Enhancement
Authors: Rossi, F. / Casazza, V. / Garavaglia, S. / Sathyasaikumar, K.V. / Schwarcz, R. / Kojima, S.I. / Okuwaki, K. / Ono, S.I. / Kajii, Y. / Rizzi, M.
History
DepositionJun 8, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KYNURENINE/ALPHA-AMINOADIPATE AMINOTRANSFERASE, MITOCHONDRIAL
B: KYNURENINE/ALPHA-AMINOADIPATE AMINOTRANSFERASE, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,2358
Polymers94,7972
Non-polymers1,4386
Water7,494416
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8950 Å2
ΔGint-61.1 kcal/mol
Surface area29690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.323, 152.857, 60.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9996, -0.00348, 0.02809), (0.01708, -0.86539, 0.49), (0.02257, 0.50109, 0.8651)
Vector: 29.79189, 71.86334, -19.65713)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein KYNURENINE/ALPHA-AMINOADIPATE AMINOTRANSFERASE, MITOCHONDRIAL / KYNURENINE AMINOTRANSFERASE II / KYNURENINE--OXOGLUTARATE AMINOTRANSFERASE II / KYNURENINE-- ...KYNURENINE AMINOTRANSFERASE II / KYNURENINE--OXOGLUTARATE AMINOTRANSFERASE II / KYNURENINE--OXOGLUTARATE TRANSAMINASE II / 2-AMINOADIPATE TRANSAMINASE / 2-AMINOADIPATE AMINOTRANSFERASE / ALPHA-AMINOADIPATE AMINOTRANSFERASE / AADAT


Mass: 47398.352 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET16B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q8N5Z0, kynurenine-oxoglutarate transaminase, 2-aminoadipate transaminase

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Non-polymers , 5 types, 422 molecules

#2: Chemical ChemComp-BF5 / (3S)-10-(4-AMINOPIPERAZIN-1-YL)-9-FLUORO-7-HYDROXY-3-METHYL-2,3-DIHYDRO-8H-[1,4]OXAZINO[2,3,4-IJ]QUINOLINE-6-CARBOXYLATE


Mass: 362.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H19FN4O4
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, MET 1 TO GLU ENGINEERED RESIDUE IN CHAIN B, MET 1 TO GLU
Nonpolymer detailsBF5-PLP: COVALENT LINK BETWEEN THE PLP COFACTOR AND THE SYNTHETIC INHIBITOR NAMED BFF-122.
Sequence detailsTHE SEGMENT 20-32 IS MISSING FROM THE COORDINATES FILE. THE FIRST RESIDUE IS A GLU THAT REPLACES A ...THE SEGMENT 20-32 IS MISSING FROM THE COORDINATES FILE. THE FIRST RESIDUE IS A GLU THAT REPLACES A MET AS A RESULT OF CLONING STRATEGY

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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: 2.41 Å3/Da / Density % sol: 48.96 % / Description: NONE
Crystal growpH: 7 / Details: pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.981
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.981 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 53172 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 5.1
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 7 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2R2N

2r2n


Resolution: 2.1→32.04 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.902 / SU B: 4.583 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24123 1113 2.1 %RANDOM
Rwork0.18814 ---
obs0.18929 53172 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.306 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å20 Å2
2---0.47 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 2.1→32.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6467 0 89 416 6972
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0226722
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7951.9879139
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9415820
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.15924.789284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.867151136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7351528
X-RAY DIFFRACTIONr_chiral_restr0.1470.21004
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025068
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2260.23051
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.24584
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2448
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2780.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1171.54174
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.88826694
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.77632906
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.3554.52445
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 68 -
Rwork0.198 3846 -
obs--100 %

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