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- PDB-12ay: Human Ornithine Aminotransferase soaked with its inhibitor,(3S,4S... -

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Basic information

Entry
Database: PDB / ID: 12ay
TitleHuman Ornithine Aminotransferase soaked with its inhibitor,(3S,4S)-3-amino-4-ethynylcyclopent-1-ene-1-carboxylic acid
ComponentsOrnithine aminotransferase, mitochondrial
KeywordsTRANSFERASE / Aminotransferase
Function / homology
Function and homology information


ornithine aminotransferase / L-ornithine transaminase activity / Glutamate and glutamine metabolism / L-glutamine catabolic process / L-proline biosynthetic process / L-glutamate catabolic process / visual perception / pyridoxal phosphate binding / mitochondrial matrix / mitochondrion / identical protein binding
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: 1.58 Å
AuthorsCorrigan, M.C. / Wang, F. / Silverman, R.B. / Liu, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: J.Am.Chem.Soc. / Year: 2026
Title: Mechanism-Based Inactivation of Human Ornithine Aminotransferase by Ethynyl- and Nitrile-Substituted Cyclopentene Analogues of gamma-Aminobutyric Acids.
Authors: Wang, F. / Corrigan, M.C. / Le, N.H.V. / Duan, D. / Smith, C.O. / Moran, G.R. / Kelleher, N.L. / Liu, D. / Silverman, R.B.
History
DepositionMar 24, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 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)147,38811
Polymers145,7813
Non-polymers1,6078
Water20,0511113
1
A: Ornithine aminotransferase, mitochondrial
hetero molecules

A: Ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,1366
Polymers97,1872
Non-polymers9494
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area12580 Å2
ΔGint-66 kcal/mol
Surface area25870 Å2
MethodPISA
2
B: Ornithine aminotransferase, mitochondrial
C: Ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,3208
Polymers97,1872
Non-polymers1,1336
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13160 Å2
ΔGint-68 kcal/mol
Surface area25600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.820, 115.820, 186.275
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-694-

HOH

21A-940-

HOH

31B-667-

HOH

41B-968-

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-A1DBA / 4-ethenyl-3-[[2-methyl-3-oxidanyl-5-[[oxidanyl-bis(oxidanylidene)-$l^{6}-phosphanyl]oxymethyl]pyridin-4-yl]methylamino]cyclopenta-1,3-diene-1-carboxylic acid


Mass: 382.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H19N2O7P / 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.: 1113 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.47 Å3/Da / Density % sol: 50.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 7.5% PEG 6000, 0.1 M NaCl, 2% glycerol, 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-F / Wavelength: 0.97872 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 6, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.58→100.303 Å / Num. obs: 176489 / % possible obs: 96.5 % / Redundancy: 20.7 % / Biso Wilson estimate: 19.28 Å2 / CC1/2: 0.999 / Net I/σ(I): 12.3
Reflection shellResolution: 1.583→1.666 Å / Num. unique obs: 8825 / CC1/2: 0.306

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→68.25 Å / SU ML: 0.1819 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.5647
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1922 8726 4.94 %
Rwork0.1681 167763 -
obs0.1693 176489 89.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.41 Å2
Refinement stepCycle: LAST / Resolution: 1.58→68.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9475 0 108 1113 10696
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01289803
X-RAY DIFFRACTIONf_angle_d1.194513315
X-RAY DIFFRACTIONf_chiral_restr0.08791464
X-RAY DIFFRACTIONf_plane_restr0.01061706
X-RAY DIFFRACTIONf_dihedral_angle_d16.36413626
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.60.218120.280371X-RAY DIFFRACTION1.14
1.6-1.620.3723370.2993657X-RAY DIFFRACTION10.74
1.62-1.640.28761120.31332163X-RAY DIFFRACTION34.98
1.64-1.660.30892030.29434148X-RAY DIFFRACTION66.92
1.66-1.680.32112640.29285407X-RAY DIFFRACTION87.5
1.68-1.710.313310.28195857X-RAY DIFFRACTION95.6
1.71-1.730.313240.27356052X-RAY DIFFRACTION97.76
1.73-1.760.30943230.25276139X-RAY DIFFRACTION99.89
1.76-1.780.29683120.2336187X-RAY DIFFRACTION100
1.78-1.810.26483100.22776195X-RAY DIFFRACTION100
1.81-1.840.24513210.22086170X-RAY DIFFRACTION100
1.84-1.880.22962990.20516190X-RAY DIFFRACTION100
1.88-1.910.21652780.19856216X-RAY DIFFRACTION100
1.91-1.950.22273460.19026152X-RAY DIFFRACTION100
1.95-1.990.20463260.18696212X-RAY DIFFRACTION100
1.99-2.040.22693000.17966187X-RAY DIFFRACTION99.98
2.04-2.090.19783270.18336203X-RAY DIFFRACTION100
2.09-2.150.20663430.17696187X-RAY DIFFRACTION100
2.15-2.210.20753200.17416177X-RAY DIFFRACTION100
2.21-2.280.20453230.16546255X-RAY DIFFRACTION100
2.28-2.360.19123100.16826233X-RAY DIFFRACTION100
2.36-2.460.19583360.16656213X-RAY DIFFRACTION100
2.46-2.570.1933720.16586169X-RAY DIFFRACTION100
2.57-2.710.18523690.1646188X-RAY DIFFRACTION100
2.71-2.880.20123490.16416225X-RAY DIFFRACTION100
2.88-3.10.17963070.15826272X-RAY DIFFRACTION100
3.1-3.410.18883360.15266309X-RAY DIFFRACTION100
3.41-3.90.14663420.13816294X-RAY DIFFRACTION100
3.9-4.920.12992780.12226428X-RAY DIFFRACTION100
4.92-68.250.15673260.14786607X-RAY DIFFRACTION99.83
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0371316643157-0.0175408864498-0.04590406658370.05491616869890.004214210603240.09149096280390.124408924845-0.08702931830870.223987191198-0.02013034895430.0437826786156-0.0568227291871-0.183246657393-8.86339175463E-50.1350948233290.1479628338120.08921366555510.1385496443260.0847405017276-0.07369469678130.307818829334-18.6429885976-5.512755592035.17622930707
20.05701745519210.004826899723350.002183214675690.0498566853757-0.02458848241720.06003814771080.0206238978060.02020516766940.0530029150628-0.02954544554140.003920446551790.00364281990705-0.00434135477905-0.2202869999730.01344317581470.05477448099670.1109051911640.01825382221290.313554266284-0.0098883794670.119282585953-56.1124295034-27.88081431480.126756814985
30.09801056500340.01791554029760.01071907301990.04349699246080.02371550227790.1006600567370.0795183689752-0.061590604679-0.02238208168430.0474284091787-0.02085336827120.007082447467520.108864850964-0.2683008057340.06031494465720.134765633732-0.0615215496441-0.002078326613280.3307050778910.01162961238760.114094904076-60.0050670815-48.764825594519.5446582554
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 36 through 439)AA36 - 4391 - 404
22(chain 'B' and resid 37 through 439)BD37 - 4391 - 403
33(chain 'C' and resid 37 through 439)CH37 - 4391 - 403

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