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- PDB-12az: Human Ornithine Aminotransferase cocrystallized with its inhibito... -

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Basic information

Entry
Database: PDB / ID: 12az
TitleHuman Ornithine Aminotransferase cocrystallized with its inhibitor, (3S,4R)-3-amino-4-cyanocyclopent-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
: / PYRIDOXAL-5'-PHOSPHATE / Ornithine aminotransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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

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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)147,15910
Polymers145,7813
Non-polymers1,3787
Water15,727873
1
A: Ornithine aminotransferase, mitochondrial
hetero molecules

A: Ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,9504
Polymers97,1872
Non-polymers7632
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area12610 Å2
ΔGint-66 kcal/mol
Surface area25980 Å2
MethodPISA
2
C: Ornithine aminotransferase, mitochondrial
hetero molecules

B: Ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,1848
Polymers97,1872
Non-polymers9976
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z+1/31
Buried area12450 Å2
ΔGint-64 kcal/mol
Surface area26120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.193, 116.193, 188.142
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-676-

HOH

21A-868-

HOH

31C-826-

HOH

41C-911-

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-A1DBG / (3Z,4R)-4-cyano-3-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]cyclopent-1-ene-1-carboxylic acid


Mass: 381.277 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H16N3O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 873 / 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: 2.51 Å3/Da / Density % sol: 51.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 8-18% PEG 6000, 0.1-0.25 M NaCl,14-20% 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: Apr 4, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.7→100.626 Å / Num. obs: 135418 / % possible obs: 95.8 % / Redundancy: 11 % / Biso Wilson estimate: 28.2 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.5
Reflection shellResolution: 1.7→1.83 Å / Num. unique obs: 6771 / CC1/2: 0.448

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→62.71 Å / SU ML: 0.1738 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.73
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.19 6753 4.99 %
Rwork0.162 128632 -
obs0.1634 135385 84.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.45 Å2
Refinement stepCycle: LAST / Resolution: 1.7→62.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9471 0 91 873 10435
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00669791
X-RAY DIFFRACTIONf_angle_d0.800313302
X-RAY DIFFRACTIONf_chiral_restr0.05511467
X-RAY DIFFRACTIONf_plane_restr0.00571709
X-RAY DIFFRACTIONf_dihedral_angle_d13.74113612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.7200.317323X-RAY DIFFRACTION0.46
1.72-1.740.307960.301139X-RAY DIFFRACTION2.79
1.74-1.770.2989320.2696426X-RAY DIFFRACTION8.71
1.77-1.790.287620.26791152X-RAY DIFFRACTION22.95
1.79-1.810.27971140.26482157X-RAY DIFFRACTION42.99
1.81-1.840.27771910.27163332X-RAY DIFFRACTION67.21
1.84-1.860.28092230.25544456X-RAY DIFFRACTION88.18
1.86-1.890.29032810.24184945X-RAY DIFFRACTION98.42
1.89-1.920.27483100.22434969X-RAY DIFFRACTION99.85
1.92-1.950.2362510.21765033X-RAY DIFFRACTION100
1.95-1.980.23482670.21235036X-RAY DIFFRACTION100
1.98-2.020.23692490.21035064X-RAY DIFFRACTION99.98
2.02-2.060.23112740.19185044X-RAY DIFFRACTION99.98
2.06-2.10.24762220.1895080X-RAY DIFFRACTION100
2.1-2.150.2052460.17355096X-RAY DIFFRACTION99.98
2.15-2.20.20382500.17345052X-RAY DIFFRACTION100
2.2-2.250.20862800.17135013X-RAY DIFFRACTION99.98
2.25-2.310.19912470.17415089X-RAY DIFFRACTION100
2.31-2.380.20072810.17655035X-RAY DIFFRACTION99.98
2.38-2.460.23142530.17955099X-RAY DIFFRACTION100
2.46-2.550.19622670.17685038X-RAY DIFFRACTION99.98
2.55-2.650.22922910.17865079X-RAY DIFFRACTION99.98
2.65-2.770.22392510.17315120X-RAY DIFFRACTION100
2.77-2.910.19172860.17115029X-RAY DIFFRACTION99.96
2.91-3.10.20142880.17315090X-RAY DIFFRACTION99.98
3.1-3.340.20072870.16585102X-RAY DIFFRACTION99.93
3.34-3.670.17922180.15195191X-RAY DIFFRACTION99.94
3.67-4.20.15462900.12655122X-RAY DIFFRACTION99.98
4.2-5.290.13912470.11925258X-RAY DIFFRACTION99.96
5.3-62.710.14412890.13915363X-RAY DIFFRACTION99.65
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)
10.995244284296-0.0850315229699-0.6523714060330.9460181650240.3082168109191.660211529380.251042921577-0.05325098073590.510395155357-0.09728854656960.0100539694633-0.112592533531-0.539215258931-0.0328215767882-0.1404697509770.2995604014630.07568968959440.1173547862040.18226927917-0.03988992182080.452592714416-18.768527618-5.709062466035.34596324368
21.13644430475-0.351644302494-0.08208696285911.143225497420.09784375308481.421967471370.0192323634053-0.1069168807960.0305452223116-0.02038179727720.0373680962713-0.2758190108010.1182885942870.620809699594-0.04810483004930.30424583270.0679093962445-0.01852956874590.4165631893750.02143582819370.211622616493-43.7518470288-27.9179535116-42.7229087801
31.0520540102-0.067394333087-0.0789814776950.695472961272-0.2160992327291.217286133260.00298857976730.08621375971120.112686681752-0.01879156483370.01704895536830.106794862572-0.0226129713776-0.336496433354-0.01042092902220.1508607882770.07132712224740.01747823026460.3820644253480.001139472768440.180749433251-56.3295054062-28.11832381620.164754331231
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 37 through 439)AA37 - 4391 - 403
22(chain 'B' and resid 36 through 439)BC36 - 4391 - 404
33(chain 'C' and resid 37 through 439)CF37 - 4391 - 403

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