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- PDB-10lw: Final Adduct of Human Ornithine Aminotransferase Inactivated by (... -

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Basic information

Entry
Database: PDB / ID: 10lw
TitleFinal Adduct of Human Ornithine Aminotransferase Inactivated by (1R,4S)-4-Amino-3-(trifluoromethyl)cyclopent-2-ene-1-carboxylic Acid
ComponentsOrnithine aminotransferase, mitochondrial
KeywordsTRANSFERASE / Aminotransferase / L-ornithine / Inactivation
Function / homology
Function and homology information


: / ornithine aminotransferase / L-ornithine transaminase activity / : / L-proline biosynthetic process / Glutamate and glutamine metabolism / visual perception / pyridoxal phosphate binding / mitochondrial matrix / mitochondrion ...: / ornithine aminotransferase / L-ornithine transaminase activity / : / L-proline biosynthetic process / Glutamate and glutamine metabolism / visual perception / pyridoxal phosphate binding / mitochondrial matrix / mitochondrion / nucleoplasm / 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
Chem-RMT / Ornithine aminotransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsVargas, A.L. / Liu, D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)DA030604 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA260250 United States
CitationJournal: Med.Chem.Res. / Year: 2026
Title: Inactivation of ornithine aminotransferase by (1 R ,4 S )-4-Amino-3-(trifluoromethyl)cyclopent-2-ene-1-carboxylic acid via a stable quinonoid intermediate.
Authors: Kang, K.M. / Vargas, A.L. / Zhu, W. / Sokolenko, I. / Liu, D. / Silverman, R.B.
History
DepositionJan 27, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)147,44211
Polymers145,7813
Non-polymers1,6618
Water8,755486
1
A: Ornithine aminotransferase, mitochondrial
hetero molecules

A: Ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,1726
Polymers97,1872
Non-polymers9854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area11090 Å2
ΔGint-59 kcal/mol
Surface area25550 Å2
MethodPISA
2
B: Ornithine aminotransferase, mitochondrial
hetero molecules

C: Ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,3568
Polymers97,1872
Non-polymers1,1696
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-y-1,x-y,z-1/31
Buried area11330 Å2
ΔGint-60 kcal/mol
Surface area25780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.485, 115.485, 187.081
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-664-

HOH

21A-764-

HOH

31C-679-

HOH

41C-775-

HOH

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Components

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


Mass: 48593.668 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-RMT / (3R,4E)-4-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]cyclopent-1-ene-1,3-dicarboxylic acid


Mass: 400.277 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H17N2O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 486 / 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: 2.47 Å3/Da / Density % sol: 50.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 7.25%-8.50% PEG 6000, 100 mM-250 mM NaCl, 2-3.5% glycerol, and 100 mM Tricine 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: 0.97872 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.93→50.01 Å / Num. obs: 102426 / % possible obs: 93.7 % / Redundancy: 6.9 % / Biso Wilson estimate: 40 Å2 / CC1/2: 1 / Net I/σ(I): 16.8
Reflection shellResolution: 1.93→1.96 Å / Num. unique obs: 102426 / CC1/2: 0.329

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→50.01 Å / SU ML: 0.245 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.7831
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2166 5215 5.09 %
Rwork0.18 97210 -
obs0.1818 102425 93.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.89 Å2
Refinement stepCycle: LAST / Resolution: 1.93→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9464 0 111 486 10061
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079795
X-RAY DIFFRACTIONf_angle_d0.853613313
X-RAY DIFFRACTIONf_chiral_restr0.05721464
X-RAY DIFFRACTIONf_plane_restr0.00771712
X-RAY DIFFRACTIONf_dihedral_angle_d16.38423610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.950.37391410.32823320X-RAY DIFFRACTION96.62
1.95-1.970.3291750.30593413X-RAY DIFFRACTION99.83
1.97-20.30882100.27863386X-RAY DIFFRACTION99.86
2-2.020.30081770.26283468X-RAY DIFFRACTION99.97
2.02-2.050.29631920.26373378X-RAY DIFFRACTION99.97
2.05-2.050.2688450.2894804X-RAY DIFFRACTION99.88
2.08-2.110.29491890.26073385X-RAY DIFFRACTION99.5
2.11-2.140.28092000.23843430X-RAY DIFFRACTION100
2.14-2.170.27011860.2433390X-RAY DIFFRACTION99.97
2.17-2.210.27031770.23023395X-RAY DIFFRACTION100
2.21-2.230.27981520.23062573X-RAY DIFFRACTION99.96
2.26-2.280.28911230.22782331X-RAY DIFFRACTION98.59
2.28-2.330.28231820.21523427X-RAY DIFFRACTION100
2.33-2.380.22691730.20213462X-RAY DIFFRACTION99.97
2.38-2.430.25481830.20843438X-RAY DIFFRACTION100
2.43-2.480.24592100.20373399X-RAY DIFFRACTION100
2.48-2.550.22131650.20063464X-RAY DIFFRACTION100
2.55-2.620.26061960.20273452X-RAY DIFFRACTION100
2.62-2.690.20741220.19442429X-RAY DIFFRACTION70.26
2.69-2.780.23571970.19833462X-RAY DIFFRACTION100
2.78-2.880.23521850.19983458X-RAY DIFFRACTION99.97
2.88-2.990.26911710.18673437X-RAY DIFFRACTION100
2.99-3.130.22671750.19893529X-RAY DIFFRACTION100
3.13-3.290.24261520.19333482X-RAY DIFFRACTION100
3.3-3.50.19521880.18313056X-RAY DIFFRACTION88.44
3.5-3.770.21741520.16533365X-RAY DIFFRACTION95.6
3.77-4.150.18451810.14993337X-RAY DIFFRACTION95.24
4.15-4.750.18662250.14173485X-RAY DIFFRACTION99.95
4.75-5.980.19532030.15233537X-RAY DIFFRACTION99.97
5.98-50.010.1581880.14533718X-RAY DIFFRACTION99.62

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