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- PDB-9y3m: Crystal Structure of Human Ornithine Aminotransferase Pre-inactiv... -

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Basic information

Entry
Database: PDB / ID: 9y3m
TitleCrystal Structure of Human Ornithine Aminotransferase Pre-inactivated by CPP115 (Covalent Inactivation)
ComponentsOrnithine aminotransferase, renal form
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: 1.73 Å
AuthorsVargas, A.L. / Kang, K.M. / Corrigan, M.C. / Liu, D. / Silverman, R.B.
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 2, 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
B: Ornithine aminotransferase, renal form
A: Ornithine aminotransferase, renal form
C: Ornithine aminotransferase, renal form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,7466
Polymers134,6233
Non-polymers1,1233
Water17,781987
1
B: Ornithine aminotransferase, renal form
C: Ornithine aminotransferase, renal form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4974
Polymers89,7492
Non-polymers7492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10560 Å2
ΔGint-64 kcal/mol
Surface area26040 Å2
MethodPISA
2
A: Ornithine aminotransferase, renal form
hetero molecules

A: Ornithine aminotransferase, renal form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4974
Polymers89,7492
Non-polymers7492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465y-1,x+1,-z1
Buried area10530 Å2
ΔGint-61 kcal/mol
Surface area26050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.332, 116.332, 188.386
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
11B-734-

HOH

21B-953-

HOH

31A-719-

HOH

41A-904-

HOH

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Components

#1: Protein Ornithine aminotransferase, renal form


Mass: 44874.348 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OAT / Plasmid: BL21DE3 / Production host: Escherichia coli (E. coli) / References: UniProt: P04181
#2: Chemical ChemComp-A1CR8 / (2S)-2-{(2Z)-2-[({6-methyl-5-oxo-3-[(phosphonooxy)methyl]-2,5-dihydropyridin-4-yl}methyl)imino]ethyl}pentanoic acid


Mass: 374.326 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C15H23N2O7P / Source: (gene. exp.) Homo sapiens (human) / Plasmid: BL21DE3 / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 987 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 54.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 10% PEG 6000, 200 mM NaCl, 18% glycerol, 100 mM tricine, pH 7.8
PH range: 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: 0.97856 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 6, 2025
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.73→100.75 Å / Num. obs: 152885 / % possible obs: 99.99 % / Redundancy: 11.1 % / Biso Wilson estimate: 23.21 Å2 / CC1/2: 0.998 / Net I/σ(I): 10.3
Reflection shellResolution: 1.73→1.83 Å / Redundancy: 10.2 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 22099 / Rpim(I) all: 0.671 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→62.8 Å / SU ML: 0.2302 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.9891
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: The coordinates of THR 322 (chain A) were transformed from an adjacent asymmetric unit, but the corresponding anisotropic displacement parameters were not updated.
RfactorNum. reflection% reflection
Rfree0.2069 7873 5.15 %
Rwork0.17 144926 -
obs0.1719 152799 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.66 Å2
Refinement stepCycle: LAST / Resolution: 1.73→62.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6051 0 3476 987 10514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0149740
X-RAY DIFFRACTIONf_angle_d1.219613216
X-RAY DIFFRACTIONf_chiral_restr0.09041470
X-RAY DIFFRACTIONf_plane_restr0.01021688
X-RAY DIFFRACTIONf_dihedral_angle_d15.50923609
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.750.36782650.33964775X-RAY DIFFRACTION100
1.75-1.770.37672840.32914748X-RAY DIFFRACTION100
1.77-1.80.32482640.30344792X-RAY DIFFRACTION100
1.8-1.820.32592380.29284829X-RAY DIFFRACTION100
1.82-1.840.27812430.27654814X-RAY DIFFRACTION100
1.84-1.870.29242590.25934736X-RAY DIFFRACTION100
1.87-1.890.28182830.2434749X-RAY DIFFRACTION100
1.89-1.920.26933090.22964764X-RAY DIFFRACTION100
1.92-1.950.2492780.2174753X-RAY DIFFRACTION100
1.95-1.980.26072750.2134808X-RAY DIFFRACTION100
1.98-2.020.24362470.20234802X-RAY DIFFRACTION99.98
2.02-2.060.2422700.19674795X-RAY DIFFRACTION100
2.06-2.10.22672950.19444762X-RAY DIFFRACTION100
2.1-2.140.20872380.18424842X-RAY DIFFRACTION100
2.14-2.180.21042240.17774826X-RAY DIFFRACTION100
2.18-2.240.22432690.17724802X-RAY DIFFRACTION100
2.24-2.290.22032460.17764828X-RAY DIFFRACTION99.98
2.29-2.350.20722780.17234777X-RAY DIFFRACTION100
2.35-2.420.22522820.17494844X-RAY DIFFRACTION100
2.42-2.50.20772630.17374763X-RAY DIFFRACTION100
2.5-2.590.21612860.16894839X-RAY DIFFRACTION100
2.59-2.690.22292460.17034862X-RAY DIFFRACTION100
2.69-2.820.18482620.16444844X-RAY DIFFRACTION100
2.82-2.960.21292650.1634852X-RAY DIFFRACTION100
2.96-3.150.19232620.16254849X-RAY DIFFRACTION100
3.15-3.390.18052240.15414912X-RAY DIFFRACTION100
3.39-3.740.18892630.14134887X-RAY DIFFRACTION100
3.74-4.280.16152380.12564941X-RAY DIFFRACTION100
4.28-5.390.15252540.12784977X-RAY DIFFRACTION100
5.39-62.80.16932630.14995154X-RAY DIFFRACTION99.76
Refinement TLS params.Method: refined / Origin x: -71.3411489456 Å / Origin y: 27.6301605338 Å / Origin z: 8.61150523848 Å
111213212223313233
T0.131294929153 Å20.0931664904531 Å2-0.0241397436142 Å2-0.234292860587 Å20.00380379498176 Å2--0.188784448242 Å2
L0.830448727614 °20.0293444515561 °20.231463650475 °2-0.380209760675 °2-0.0351569033901 °2--0.835723944985 °2
S0.0802241658044 Å °0.0211550845722 Å °-0.130860423129 Å °0.0161005401891 Å °-0.0114625525974 Å °-0.0240280303743 Å °0.0084977766992 Å °0.246407080746 Å °-0.0350972829126 Å °
Refinement TLS groupSelection details: all

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