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- PDB-10lx: High Stable Quinonoid Intermediate of Human Ornithine Aminotransf... -

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Basic information

Entry
Database: PDB / ID: 10lx
TitleHigh Stable Quinonoid Intermediate of Human Ornithine Aminotransferase Complexed with (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
: / Ornithine aminotransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 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

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)147,0066
Polymers145,7813
Non-polymers1,2253
Water15,853880
1
A: Ornithine aminotransferase, mitochondrial
C: Ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,0044
Polymers97,1872
Non-polymers8172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10410 Å2
ΔGint-62 kcal/mol
Surface area25840 Å2
MethodPISA
2
B: Ornithine aminotransferase, mitochondrial
hetero molecules

B: Ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,0044
Polymers97,1872
Non-polymers8172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area10410 Å2
ΔGint-61 kcal/mol
Surface area25880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.520, 115.520, 187.440
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-897-

HOH

21B-695-

HOH

31B-894-

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-A1C6V / (1S,4R)-4-(difluoromethyl)-3-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]cyclopent-2-ene-1-carboxylic acid


Mass: 408.291 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H19F2N2O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 880 / 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: 2.48 Å3/Da / Density % sol: 50.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
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-D / Wavelength: 0.920105 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 26, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920105 Å / Relative weight: 1
ReflectionResolution: 1.83→34.2 Å / Num. obs: 128275 / % possible obs: 99.98 % / Redundancy: 19 % / Biso Wilson estimate: 25.5 Å2 / CC1/2: 0.999 / Net I/σ(I): 12.7
Reflection shellResolution: 1.83→1.858 Å / Num. unique obs: 6311 / CC1/2: 0.426

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→34.2 Å / SU ML: 0.256 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.6002
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2339 6380 4.97 %
Rwork0.1989 121895 -
obs0.2007 128275 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.83 Å2
Refinement stepCycle: LAST / Resolution: 1.83→34.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9483 0 81 880 10444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00659789
X-RAY DIFFRACTIONf_angle_d0.838813308
X-RAY DIFFRACTIONf_chiral_restr0.05371464
X-RAY DIFFRACTIONf_plane_restr0.00651710
X-RAY DIFFRACTIONf_dihedral_angle_d15.10973675
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.850.35132390.31543994X-RAY DIFFRACTION99.88
1.85-1.870.32991850.3144029X-RAY DIFFRACTION99.88
1.87-1.890.33752020.30414043X-RAY DIFFRACTION99.98
1.89-1.920.32262330.28943995X-RAY DIFFRACTION99.98
1.92-1.940.32662100.28793993X-RAY DIFFRACTION100
1.94-1.970.3442270.27694026X-RAY DIFFRACTION99.98
1.97-20.30621980.27794039X-RAY DIFFRACTION100
2-2.030.30182230.27284040X-RAY DIFFRACTION100
2.03-2.060.31691780.27284057X-RAY DIFFRACTION100
2.06-2.090.32422520.26333960X-RAY DIFFRACTION100
2.09-2.130.29662190.25484023X-RAY DIFFRACTION99.98
2.13-2.170.30571920.24534056X-RAY DIFFRACTION100
2.17-2.210.28492160.24294024X-RAY DIFFRACTION100
2.21-2.250.2761970.24184067X-RAY DIFFRACTION100
2.25-2.30.26131960.23624065X-RAY DIFFRACTION100
2.3-2.360.311780.22574082X-RAY DIFFRACTION100
2.36-2.410.24661980.22584051X-RAY DIFFRACTION100
2.41-2.480.29252540.23163990X-RAY DIFFRACTION100
2.48-2.550.26482240.22264036X-RAY DIFFRACTION100
2.55-2.640.261890.21954116X-RAY DIFFRACTION100
2.64-2.730.23281950.2134049X-RAY DIFFRACTION100
2.73-2.840.25692050.20484074X-RAY DIFFRACTION100
2.84-2.970.22452500.19824063X-RAY DIFFRACTION100
2.97-3.120.21882100.19264088X-RAY DIFFRACTION100
3.12-3.320.22782180.18944062X-RAY DIFFRACTION100
3.32-3.580.2152070.18174101X-RAY DIFFRACTION99.98
3.58-3.930.20862230.164115X-RAY DIFFRACTION100
3.94-4.50.1712090.1444144X-RAY DIFFRACTION100
4.5-5.670.1612320.13584156X-RAY DIFFRACTION99.98
5.67-34.20.15972210.14834357X-RAY DIFFRACTION99.87

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