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- PDB-9y53: Crystal Structure of Human Ornithine Aminotransferase Soaked with... -

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Basic information

Entry
Database: PDB / ID: 9y53
TitleCrystal Structure of Human Ornithine Aminotransferase Soaked with CPP115
ComponentsOrnithine aminotransferase, mitochondrial
KeywordsTRANSFERASE / Mechanism based inactivator / aminotransferase
Function / homology
Function and homology information


: / ornithine aminotransferase / L-ornithine transaminase activity / : / Glutamate and glutamine metabolism / L-proline biosynthetic process / visual perception / pyridoxal phosphate binding / mitochondrial matrix / mitochondrion ...: / ornithine aminotransferase / L-ornithine transaminase activity / : / Glutamate and glutamine metabolism / L-proline biosynthetic process / visual perception / pyridoxal phosphate binding / mitochondrial matrix / mitochondrion / identical protein binding / cytoplasm
Similarity search - Function
Ornithine aminotransferase / : / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
: / Ornithine aminotransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsCorrigan, M.C. / Vargas, A.L. / Kang, K.M. / Silverman, R.B. / Liu, D.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 DA030604 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA260250 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P41 GM108569 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30 DA018310 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2026
Title: Targeting Conformational Flexibility of a Reactive Intermediate to Enhance Selectivity of a GABA Aminotransferase Inactivator.
Authors: Kang, K.M. / Vargas, A.L. / Ferreira, L.A. / Des Soye, B.J. / Corrigan, M. / Zhang, C.K. / Wang, F. / Duan, D. / Kelleher, N.L. / Hohmann, A.G. / Liu, D. / Silverman, R.B.
History
DepositionSep 4, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ornithine aminotransferase, mitochondrial
B: Ornithine aminotransferase, mitochondrial
C: Ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,8006
Polymers134,5813
Non-polymers1,2193
Water16,286904
1
A: Ornithine aminotransferase, mitochondrial
hetero molecules

A: Ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,5334
Polymers89,7212
Non-polymers8132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area12270 Å2
ΔGint-58 kcal/mol
Surface area25960 Å2
MethodPISA
2
B: Ornithine aminotransferase, mitochondrial
C: Ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,5334
Polymers89,7212
Non-polymers8132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12270 Å2
ΔGint-55 kcal/mol
Surface area25680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.141, 116.141, 188.375
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-685-

HOH

21A-860-

HOH

31B-907-

HOH

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Components

#1: Protein Ornithine aminotransferase, mitochondrial / Ornithine delta-aminotransferase / Ornithine--oxo-acid aminotransferase


Mass: 44860.320 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OAT / Production host: Escherichia coli (E. coli) / References: UniProt: P04181, ornithine aminotransferase
#2: Chemical ChemComp-A1CSF / (1S,4E)-3-(difluoromethylidene)-4-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]cyclopentane-1-carboxylic acid


Mass: 406.275 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H17F2N2O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 904 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.73 Å3/Da / Density % sol: 54.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 16% PEG 6000, 100 mM NaCl, 14% glycerol, pH 7.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 25, 2025
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.95→100.58 Å / Num. obs: 108192 / % possible obs: 100 % / Redundancy: 14.8 % / Biso Wilson estimate: 27.75 Å2 / CC1/2: 0.996 / Net I/σ(I): 10.3
Reflection shellResolution: 1.95→2.05 Å / Num. unique obs: 15627 / CC1/2: 0.787

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROCdata reduction
autoPROCdata scaling
PHASER1.21.2_5419phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→55.49 Å / SU ML: 0.2109 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.9781
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2184 5515 5.1 %
Rwork0.1793 102606 -
obs0.1813 108121 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.59 Å2
Refinement stepCycle: LAST / Resolution: 1.95→55.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9483 0 81 904 10468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069789
X-RAY DIFFRACTIONf_angle_d0.784713308
X-RAY DIFFRACTIONf_chiral_restr0.05391470
X-RAY DIFFRACTIONf_plane_restr0.00661719
X-RAY DIFFRACTIONf_dihedral_angle_d15.12893621
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.970.30912100.26653402X-RAY DIFFRACTION100
1.97-1.990.26151700.24163360X-RAY DIFFRACTION100
1.99-2.020.31921670.23783392X-RAY DIFFRACTION100
2.02-2.040.29012030.2273366X-RAY DIFFRACTION100
2.04-2.070.26191620.22883410X-RAY DIFFRACTION100
2.07-2.10.26851690.22483392X-RAY DIFFRACTION100
2.1-2.130.25541700.21333363X-RAY DIFFRACTION100
2.13-2.160.28831990.20963393X-RAY DIFFRACTION100
2.16-2.190.22511870.19723419X-RAY DIFFRACTION100
2.19-2.230.24561630.20133373X-RAY DIFFRACTION100
2.23-2.270.22711920.19953382X-RAY DIFFRACTION100
2.27-2.310.22411810.19143407X-RAY DIFFRACTION100
2.31-2.350.25551650.19143405X-RAY DIFFRACTION100
2.35-2.40.23411840.18923396X-RAY DIFFRACTION100
2.4-2.450.25941650.18963424X-RAY DIFFRACTION100
2.45-2.510.21191600.18563413X-RAY DIFFRACTION100
2.51-2.570.23791850.18753426X-RAY DIFFRACTION100
2.57-2.640.23372070.18783384X-RAY DIFFRACTION100
2.64-2.720.22241760.1983399X-RAY DIFFRACTION100
2.72-2.810.24661780.19813399X-RAY DIFFRACTION100
2.81-2.910.26342250.19413414X-RAY DIFFRACTION100
2.91-3.020.2261860.19353386X-RAY DIFFRACTION100
3.02-3.160.24772040.18763423X-RAY DIFFRACTION100
3.16-3.330.22411700.18043442X-RAY DIFFRACTION100
3.33-3.540.19121570.17643483X-RAY DIFFRACTION100
3.54-3.810.21122080.15743409X-RAY DIFFRACTION100
3.81-4.190.17541790.15043492X-RAY DIFFRACTION100
4.19-4.80.16851870.14243479X-RAY DIFFRACTION100
4.8-6.040.18851860.15383520X-RAY DIFFRACTION100
6.05-55.490.18362200.15953653X-RAY DIFFRACTION99.97
Refinement TLS params.Method: refined / Origin x: -44.9338858271 Å / Origin y: -27.5379865493 Å / Origin z: 8.47044103485 Å
111213212223313233
T0.157010746828 Å20.117753770576 Å20.0330314640026 Å2-0.289809250167 Å2-0.00208953837027 Å2--0.206066532938 Å2
L0.759791362779 °20.0678450060621 °2-0.199415560089 °2-0.367077380111 °2-0.00126681704357 °2--0.827440728766 °2
S0.0681860350042 Å °-0.0184491985776 Å °0.147942327887 Å °0.00267883929435 Å °0.000598743581329 Å °0.0155077587977 Å °0.0119313931785 Å °-0.244611907351 Å °-0.0419740289851 Å °
Refinement TLS groupSelection details: all

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