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1gbn

HUMAN ORNITHINE AMINOTRANSFERASE COMPLEXED WITH THE NEUROTOXIN GABACULINE

Method: X-RAY DIFFRACTION Dmax: 117.0 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

ORNITHINE AMINOTRANSFERASE

Homo sapiens

UniProt P04181

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 38–439 Chain B； UniProt 38–439 Chain C； UniProt 38–439 Not recorded GAB 3-AMINOBENZOIC ACID × 1 PLP PYRIDOXAL-5'-PHOSPHATE × 3 GBC GABACULINE × 2 X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.5 Resolution 2.30 Å R-free 0.235
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 38–439 Chain B； UniProt 38–439 Not recorded GAB 3-AMINOBENZOIC ACID × 1 PLP PYRIDOXAL-5'-PHOSPHATE × 2 GBC GABACULINE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.5 Resolution 2.30 Å R-free 0.235
3 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 38–439 Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 2 GBC GABACULINE × 2 X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.5 Resolution 2.30 Å R-free 0.235
4 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 38–439 Chain B； UniProt 38–439 Chain C； UniProt 38–439 Not recorded GAB 3-AMINOBENZOIC ACID × 1 PLP PYRIDOXAL-5'-PHOSPHATE × 4 GBC GABACULINE × 3 X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.5 Resolution 2.30 Å R-free 0.235

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1GBN Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
10LW Final Adduct of Human Ornithine Aminotransferase Inactivated by (1R,4S)-4-Amino-3-(trifluoromethyl)cyclopent-2-ene-1-carboxylic Acid Deposited 2026-01-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–439（439 aa）
Not recorded RMT (3R,4E)-4-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]cyclopent-1-ene-1,3-dicarboxylic acid × 2 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；298 K；7.25%-8.50% PEG 6000, 100 mM-250 mM NaCl, 2-3.5% glycerol, and 100 mM Tricine pH 7.8.
Resolution 1.93 Å R-free 0.217
10LW Final Adduct of Human Ornithine Aminotransferase Inactivated by (1R,4S)-4-Amino-3-(trifluoromethyl)cyclopent-2-ene-1-carboxylic Acid Deposited 2026-01-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 1–439（439 aa）
Chain C 1–439（439 aa）
Not recorded RMT (3R,4E)-4-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]cyclopent-1-ene-1,3-dicarboxylic acid × 2 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；298 K；7.25%-8.50% PEG 6000, 100 mM-250 mM NaCl, 2-3.5% glycerol, and 100 mM Tricine pH 7.8.
Resolution 1.93 Å R-free 0.217
10LX High Stable Quinonoid Intermediate of Human Ornithine Aminotransferase Complexed with (1R,4S)-4-Amino-3-(trifluoromethyl)cyclopent-2-ene-1-carboxylic Acid Deposited 2026-01-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–439（439 aa）
Chain C 1–439（439 aa）
Not recorded A1C6V (1S,4R)-4-(difluoromethyl)-3-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]cyclopent-2-ene-1-carboxylic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；7.25%-8.50% PEG 6000, 100 mM-250 mM NaCl, 2-3.5% glycerol, and 100 mM Tricine pH 7.8.
Resolution 1.83 Å R-free 0.234
10LX High Stable Quinonoid Intermediate of Human Ornithine Aminotransferase Complexed with (1R,4S)-4-Amino-3-(trifluoromethyl)cyclopent-2-ene-1-carboxylic Acid Deposited 2026-01-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 1–439（439 aa）
Not recorded A1C6V (1S,4R)-4-(difluoromethyl)-3-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]cyclopent-2-ene-1-carboxylic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；7.25%-8.50% PEG 6000, 100 mM-250 mM NaCl, 2-3.5% glycerol, and 100 mM Tricine pH 7.8.
Resolution 1.83 Å R-free 0.234
1OAT ORNITHINE AMINOTRANSFERASE Deposited 1997-03-26 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–439（439 aa）
Chain B 1–439（439 aa）
Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；pH 7.8
Resolution 2.50 Å R-free 0.235
1OAT ORNITHINE AMINOTRANSFERASE Deposited 1997-03-26 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–439（439 aa）
Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；pH 7.8
Resolution 2.50 Å R-free 0.235
2BYJ Ornithine aminotransferase mutant Y85I Deposited 2005-08-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–439（439 aa）
Chain B 1–439（439 aa）
Mutation：YES Mutation：YES PLP PYRIDOXAL-5'-PHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.9；6-10%PEG6000, 120-160MM NACL, 50MM TRICINE PH7.9, 1MM DTT, pH 7.90
Resolution 3.02 Å R-free 0.226
2BYJ Ornithine aminotransferase mutant Y85I Deposited 2005-08-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–439（439 aa）
Mutation：YES PLP PYRIDOXAL-5'-PHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.9；6-10%PEG6000, 120-160MM NACL, 50MM TRICINE PH7.9, 1MM DTT, pH 7.90
Resolution 3.02 Å R-free 0.226
2BYL Structure of ornithine aminotransferase triple mutant Y85I Y55A G320F Deposited 2005-08-03 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–439（439 aa）
Chain B 1–439（439 aa）
Mutation：YES Mutation：YES PLP PYRIDOXAL-5'-PHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.9；6-10%PEG6000, 120-160MM NACL, 50MM TRICINE PH7.9, 1MM DTT, pH 7.90
Resolution 2.15 Å R-free 0.191
2BYL Structure of ornithine aminotransferase triple mutant Y85I Y55A G320F Deposited 2005-08-03 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–439（439 aa）
Mutation：YES PLP PYRIDOXAL-5'-PHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.9；6-10%PEG6000, 120-160MM NACL, 50MM TRICINE PH7.9, 1MM DTT, pH 7.90
Resolution 2.15 Å R-free 0.191
2CAN HUMAN ORNITHINE AMINOTRANSFERASE COMPLEXED WITH L-CANALINE Deposited 1997-05-29 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 38–439（402 aa）
Chain B 38–439（402 aa）
Not recorded CAN CANALINE × 2 PLP PYRIDOXAL-5'-PHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.5
Resolution 2.30 Å R-free 0.238
2CAN HUMAN ORNITHINE AMINOTRANSFERASE COMPLEXED WITH L-CANALINE Deposited 1997-05-29 Different ligand/ion Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 38–439（402 aa）
Not recorded CAN CANALINE × 2 PLP PYRIDOXAL-5'-PHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.5
Resolution 2.30 Å R-free 0.238
2OAT ORNITHINE AMINOTRANSFERASE COMPLEXED WITH 5-FLUOROMETHYLORNITHINE Deposited 1998-05-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–439（439 aa）
Chain B 1–439（439 aa）
Chain C 1–439（439 aa）
Not recorded PFM 1-AMINO-7-(2-METHYL-3-OXIDO-5-((PHOSPHONOXY)METHYL)-4-PYRIDOXAL-5-OXO-6-HEPTENATE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.9；(2S,5S)5FMORN-OAT WAS CO-CRYSTALLIZED FROM 6-10% PEG 6000, 1MM DTT, 120-160 MM NACL, 10-20% GLYCEROL, 50 MM TRICIN, PH 7.9.
Resolution 1.95 Å R-free 0.232
2OAT ORNITHINE AMINOTRANSFERASE COMPLEXED WITH 5-FLUOROMETHYLORNITHINE Deposited 1998-05-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–439（439 aa）
Chain B 1–439（439 aa）
Not recorded PFM 1-AMINO-7-(2-METHYL-3-OXIDO-5-((PHOSPHONOXY)METHYL)-4-PYRIDOXAL-5-OXO-6-HEPTENATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.9；(2S,5S)5FMORN-OAT WAS CO-CRYSTALLIZED FROM 6-10% PEG 6000, 1MM DTT, 120-160 MM NACL, 10-20% GLYCEROL, 50 MM TRICIN, PH 7.9.
Resolution 1.95 Å R-free 0.232
2OAT ORNITHINE AMINOTRANSFERASE COMPLEXED WITH 5-FLUOROMETHYLORNITHINE Deposited 1998-05-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–439（439 aa）
Not recorded PFM 1-AMINO-7-(2-METHYL-3-OXIDO-5-((PHOSPHONOXY)METHYL)-4-PYRIDOXAL-5-OXO-6-HEPTENATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.9；(2S,5S)5FMORN-OAT WAS CO-CRYSTALLIZED FROM 6-10% PEG 6000, 1MM DTT, 120-160 MM NACL, 10-20% GLYCEROL, 50 MM TRICIN, PH 7.9.
Resolution 1.95 Å R-free 0.232
5VWO Ornithine aminotransferase inactivated by (1R,3S,4S)-3-amino-4-fluorocyclopentane-1-carboxylic acid (FCP) Deposited 2017-05-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 36–439（404 aa） Fragment：UNP residues 36-439
Chain B 36–439（404 aa） Fragment：UNP residues 36-439
Chain C 36–439（404 aa） Fragment：UNP residues 36-439
Not recorded 9QJ (1S,3S,4E)-3-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-4-iminocyclopentane-1-carboxylic acid × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；NaCl (175mM), 8-10% (v/v) PEG 6000
Resolution 1.77 Å R-free 0.210
6HX7 Crystal structure of human R180T variant of ORNITHINE AMINOTRANSFERASE at 1.8 Angstrom Deposited 2018-10-16 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 26–439（414 aa）
Mutation：R180T, A25M PLP PYRIDOXAL-5'-PHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；294 K；Prot 115uM in 150mM NaCl 50mM Hepes pH 8.0 mixed with hit 1-5 of the LMB screen (Molecular Dimensions): 4 M Ammonium acetate 0.1 M Bis-Tris propane 7.0 (cryo + Glycerol 20%)
Resolution 1.80 Å R-free 0.228
6HX7 Crystal structure of human R180T variant of ORNITHINE AMINOTRANSFERASE at 1.8 Angstrom Deposited 2018-10-16 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 26–439（414 aa）
Mutation：R180T, A25M PLP PYRIDOXAL-5'-PHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；294 K；Prot 115uM in 150mM NaCl 50mM Hepes pH 8.0 mixed with hit 1-5 of the LMB screen (Molecular Dimensions): 4 M Ammonium acetate 0.1 M Bis-Tris propane 7.0 (cryo + Glycerol 20%)
Resolution 1.80 Å R-free 0.228
6HX7 Crystal structure of human R180T variant of ORNITHINE AMINOTRANSFERASE at 1.8 Angstrom Deposited 2018-10-16 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 26–439（414 aa）
Mutation：R180T, A25M PLP PYRIDOXAL-5'-PHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；294 K；Prot 115uM in 150mM NaCl 50mM Hepes pH 8.0 mixed with hit 1-5 of the LMB screen (Molecular Dimensions): 4 M Ammonium acetate 0.1 M Bis-Tris propane 7.0 (cryo + Glycerol 20%)
Resolution 1.80 Å R-free 0.228
6OIA (1S,3S)-3-amino-4-(perfluoropropan-2-ylidene)cyclopentane-1-carboxylic acid hydrochloride, a potent inhibitor of ornithine aminotransferase Deposited 2019-04-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 36–439（404 aa）
Chain B 36–439（404 aa）
Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 2 GOL GLYCEROL × 2 MQ4 (1S)-3-amino-4-[(2S)-1,1,1-trifluoro-3-oxopropan-2-yl]cyclopent-3-ene-1-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；10% PEG 6000, 200 mM NaCl, 2.5 % Glycerol
Resolution 1.78 Å R-free 0.189
6OIA (1S,3S)-3-amino-4-(perfluoropropan-2-ylidene)cyclopentane-1-carboxylic acid hydrochloride, a potent inhibitor of ornithine aminotransferase Deposited 2019-04-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 36–439（404 aa）
Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 2 MQ4 (1S)-3-amino-4-[(2S)-1,1,1-trifluoro-3-oxopropan-2-yl]cyclopent-3-ene-1-carboxylic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；10% PEG 6000, 200 mM NaCl, 2.5 % Glycerol
Resolution 1.78 Å R-free 0.189
6V8C Design, Synthesis, and Mechanism of Fluorine-substituted Cyclohexene Analogues of GAMA-Aminobutyric Acid (GABA) as Selective Ornithine Aminotransferase Inactivators Deposited 2019-12-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 36–439（404 aa）
Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 2 QRM 3-aminocyclohexa-1,3-diene-1-carboxylic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；16.5% PEG 1000 240 mM NaCl 25% glycerol.
Resolution 1.90 Å R-free 0.268
6V8C Design, Synthesis, and Mechanism of Fluorine-substituted Cyclohexene Analogues of GAMA-Aminobutyric Acid (GABA) as Selective Ornithine Aminotransferase Inactivators Deposited 2019-12-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 36–439（404 aa）
Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 2 QRM 3-aminocyclohexa-1,3-diene-1-carboxylic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；16.5% PEG 1000 240 mM NaCl 25% glycerol.
Resolution 1.90 Å R-free 0.268
6V8C Design, Synthesis, and Mechanism of Fluorine-substituted Cyclohexene Analogues of GAMA-Aminobutyric Acid (GABA) as Selective Ornithine Aminotransferase Inactivators Deposited 2019-12-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 36–439（404 aa）
Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 2 QRM 3-aminocyclohexa-1,3-diene-1-carboxylic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；16.5% PEG 1000 240 mM NaCl 25% glycerol.
Resolution 1.90 Å R-free 0.268
6V8D Design, Synthesis, and Mechanism of Fluorine-substituted Cyclohexene Analogues of GAMA-Aminobutyric Acid (GABA) as Selective Ornithine Aminotransferase Inactivators Deposited 2019-12-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 36–439（404 aa）
Chain B 36–439（404 aa）
Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 2 O78 (3Z)-3-iminocyclohex-1-ene-1-carboxylic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；298 K；16.5% PEG 1000 240 mM NaCl 25% glycerol 50 mM Tricine pH 7.8
Resolution 2.25 Å R-free 0.196
6V8D Design, Synthesis, and Mechanism of Fluorine-substituted Cyclohexene Analogues of GAMA-Aminobutyric Acid (GABA) as Selective Ornithine Aminotransferase Inactivators Deposited 2019-12-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 36–439（404 aa）
Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 2 O78 (3Z)-3-iminocyclohex-1-ene-1-carboxylic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；298 K；16.5% PEG 1000 240 mM NaCl 25% glycerol 50 mM Tricine pH 7.8
Resolution 2.25 Å R-free 0.196
7JX9 The crystal structure of human ornithine aminotransferase with an intermediate bound during inactivation by (1S,3S)-3-amino-4-(hexafluoropropan-2-ylidenyl)-cyclopentane-1-carboxylic acid. Deposited 2020-08-26 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 36–439（404 aa）
Not recorded IF1 (1S,3S,4S)-3-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-4-(1,1,3,3,3-pentafluoroprop-1-en-2-yl)cyclopentane-1-carboxylic acid × 2 VLS N-[1,3-dihydroxy-2-(hydroxymethyl)propan-2-yl]glycine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；290 K；10% PEG 6000, 100 mM NaCl, and 10% glycerol, Tricine 100 mM, pH 7.8
Resolution 1.96 Å R-free 0.213
7JX9 The crystal structure of human ornithine aminotransferase with an intermediate bound during inactivation by (1S,3S)-3-amino-4-(hexafluoropropan-2-ylidenyl)-cyclopentane-1-carboxylic acid. Deposited 2020-08-26 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 36–439（404 aa）
Chain C 36–439（404 aa）
Not recorded IF1 (1S,3S,4S)-3-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-4-(1,1,3,3,3-pentafluoroprop-1-en-2-yl)cyclopentane-1-carboxylic acid × 2 VLS N-[1,3-dihydroxy-2-(hydroxymethyl)propan-2-yl]glycine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；290 K；10% PEG 6000, 100 mM NaCl, and 10% glycerol, Tricine 100 mM, pH 7.8
Resolution 1.96 Å R-free 0.213
7LK0 Ornithine Aminotransferase (OAT) cocrystallized with its potent inhibitor - (S)-3-amino-4,4-difluorocyclopent-1-enecarboxylic acid (SS-1-148) Deposited 2021-02-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 36–439（404 aa）
Not recorded Y3D (1R,3S)-3-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-4-oxocyclopentane-1-carboxylic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；OAT was buffer exchanged into crystallization buffer (50 mM Tricine pH 7.8) supplied with 1 mM 2-ketoglutarate. Then the protein was concentrated to 6 mg/mL. For each hanging drop, 2 uL of protein solution was mixed with an equal volume of well solution and 0.5 uL of 10 mM SS-1-148. The crystals with the best morphology and size grew in a final condition containing 10% PEG 6000, 200 mM NaCl, 10% glycerol, 100 mM Tricine pH 7.8.
Resolution 1.96 Å R-free 0.268
7LK0 Ornithine Aminotransferase (OAT) cocrystallized with its potent inhibitor - (S)-3-amino-4,4-difluorocyclopent-1-enecarboxylic acid (SS-1-148) Deposited 2021-02-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 36–439（404 aa）
Not recorded Y3D (1R,3S)-3-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-4-oxocyclopentane-1-carboxylic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；OAT was buffer exchanged into crystallization buffer (50 mM Tricine pH 7.8) supplied with 1 mM 2-ketoglutarate. Then the protein was concentrated to 6 mg/mL. For each hanging drop, 2 uL of protein solution was mixed with an equal volume of well solution and 0.5 uL of 10 mM SS-1-148. The crystals with the best morphology and size grew in a final condition containing 10% PEG 6000, 200 mM NaCl, 10% glycerol, 100 mM Tricine pH 7.8.
Resolution 1.96 Å R-free 0.268
7LK0 Ornithine Aminotransferase (OAT) cocrystallized with its potent inhibitor - (S)-3-amino-4,4-difluorocyclopent-1-enecarboxylic acid (SS-1-148) Deposited 2021-02-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 36–439（404 aa）
Not recorded Y3D (1R,3S)-3-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-4-oxocyclopentane-1-carboxylic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；OAT was buffer exchanged into crystallization buffer (50 mM Tricine pH 7.8) supplied with 1 mM 2-ketoglutarate. Then the protein was concentrated to 6 mg/mL. For each hanging drop, 2 uL of protein solution was mixed with an equal volume of well solution and 0.5 uL of 10 mM SS-1-148. The crystals with the best morphology and size grew in a final condition containing 10% PEG 6000, 200 mM NaCl, 10% glycerol, 100 mM Tricine pH 7.8.
Resolution 1.96 Å R-free 0.268
7LK1 Ornithine Aminotransferase (OAT) with its potent inhibitor - (S)-3-amino-4,4-difluorocyclopent-1-enecarboxylic acid (SS-1-148) - 1 Hour Soaking Deposited 2021-02-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 36–439（404 aa）
Not recorded Y37 (1R,4R)-4-fluoro-3-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]cyclopent-2-ene-1-carboxylic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；The holoenzyme crystals were first grown via a hanging drop vapor diffusion method. Each drop contained 2 uL of protein and 2 uL of well solution. The best crystallization condition contained 10% PEG 6000, 200 mM NaCl, 10% glycerol, 100 mM Tricine pH 7.8. Once the holoenzyme crystals reached their maximum size, 2 uL of 16 mM SS-1-148 was added to the drop with crystals. The crystals were soaked for 1 h, transferred into cryoprotective solution (well solution supplemented with 30% glycerol), and then flash-frozen in liquid nitrogen.
Resolution 1.79 Å R-free 0.241
7LK1 Ornithine Aminotransferase (OAT) with its potent inhibitor - (S)-3-amino-4,4-difluorocyclopent-1-enecarboxylic acid (SS-1-148) - 1 Hour Soaking Deposited 2021-02-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 36–439（404 aa）
Chain C 36–439（404 aa）
Not recorded Y37 (1R,4R)-4-fluoro-3-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]cyclopent-2-ene-1-carboxylic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；The holoenzyme crystals were first grown via a hanging drop vapor diffusion method. Each drop contained 2 uL of protein and 2 uL of well solution. The best crystallization condition contained 10% PEG 6000, 200 mM NaCl, 10% glycerol, 100 mM Tricine pH 7.8. Once the holoenzyme crystals reached their maximum size, 2 uL of 16 mM SS-1-148 was added to the drop with crystals. The crystals were soaked for 1 h, transferred into cryoprotective solution (well solution supplemented with 30% glycerol), and then flash-frozen in liquid nitrogen.
Resolution 1.79 Å R-free 0.241
7LNM Ornithine Aminotransferase (OAT) cocrystallized with its inactivator - (1S,3S)-3-amino-4-(difluoromethylene)cyclopentene-1-carboxylic acid Deposited 2021-02-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 36–439（404 aa）
Chain C 36–439（404 aa）
Not recorded Y7S (1~{R},3~{S},4~{R})-3-methyl-4-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]cyclopentane-1-carboxylic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；The freshly prepared enzyme was buffer exchanged into 50 mM Tricine pH 7.8 and concentrated to a protein concentration of 6 mg/mL. For each hanging drop, 2 ul of protein solution was mixed with equal volume of well solution and 0.5 ul of 10 mM compound. The crystals with the best morphology and size grew in a final condition containing 12% PEG 8000, 200 mM NaCl, 10% glycerol, 50 mM Tricine pH 7.8.
Resolution 2.00 Å R-free 0.186
7LNM Ornithine Aminotransferase (OAT) cocrystallized with its inactivator - (1S,3S)-3-amino-4-(difluoromethylene)cyclopentene-1-carboxylic acid Deposited 2021-02-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 36–439（404 aa）
Chain F 36–439（404 aa）
Not recorded Y7S (1~{R},3~{S},4~{R})-3-methyl-4-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]cyclopentane-1-carboxylic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；The freshly prepared enzyme was buffer exchanged into 50 mM Tricine pH 7.8 and concentrated to a protein concentration of 6 mg/mL. For each hanging drop, 2 ul of protein solution was mixed with equal volume of well solution and 0.5 ul of 10 mM compound. The crystals with the best morphology and size grew in a final condition containing 12% PEG 8000, 200 mM NaCl, 10% glycerol, 50 mM Tricine pH 7.8.
Resolution 2.00 Å R-free 0.186
7LNM Ornithine Aminotransferase (OAT) cocrystallized with its inactivator - (1S,3S)-3-amino-4-(difluoromethylene)cyclopentene-1-carboxylic acid Deposited 2021-02-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain I 36–439（404 aa）
Chain J 36–439（404 aa）
Not recorded Y7S (1~{R},3~{S},4~{R})-3-methyl-4-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]cyclopentane-1-carboxylic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；The freshly prepared enzyme was buffer exchanged into 50 mM Tricine pH 7.8 and concentrated to a protein concentration of 6 mg/mL. For each hanging drop, 2 ul of protein solution was mixed with equal volume of well solution and 0.5 ul of 10 mM compound. The crystals with the best morphology and size grew in a final condition containing 12% PEG 8000, 200 mM NaCl, 10% glycerol, 50 mM Tricine pH 7.8.
Resolution 2.00 Å R-free 0.186
7LOM Ornithine Aminotransferase (OAT) soaked with its inactivator - (1S,3S)-3-amino-4-(difluoromethylene)cyclohexene-1-carboxylic acid Deposited 2021-02-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 36–439（404 aa）
Not recorded THR THREONINE × 2 Y8P (3~{S},4~{S})-4-methyl-3-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]cyclohexene-1-carboxylic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；The holoenzyme crystals were first grown via a hanging drop vapor diffusion method. Each drop contained 2 uL of protein and 2 uL of well solution. The best crystallization condition contained 8% PEG 6000, 100 mM NaCl, 5% glycerol, and 50 mM Tricine pH 7.8. Once the holoenzyme crystals reached their maximum size within five days, 1 uL of 10 mM 181 was added to the drop with crystals. Within the first three minutes of 181 addition, the hOAT crystals turned their color from yellow to transparent. The crystals were soaked for 44 minutes, transferred into cryoprotective solution (well solution supplemented with 30% glycerol), and then flash-frozen in liquid nitrogen.
Resolution 2.10 Å R-free 0.235
7LOM Ornithine Aminotransferase (OAT) soaked with its inactivator - (1S,3S)-3-amino-4-(difluoromethylene)cyclohexene-1-carboxylic acid Deposited 2021-02-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 36–439（404 aa）
Chain C 36–439（404 aa）
Not recorded THR THREONINE × 2 Y8P (3~{S},4~{S})-4-methyl-3-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]cyclohexene-1-carboxylic acid × 1 YCD (4~{R})-4-(fluoranylmethyl)-3-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]cyclohexene-1-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；The holoenzyme crystals were first grown via a hanging drop vapor diffusion method. Each drop contained 2 uL of protein and 2 uL of well solution. The best crystallization condition contained 8% PEG 6000, 100 mM NaCl, 5% glycerol, and 50 mM Tricine pH 7.8. Once the holoenzyme crystals reached their maximum size within five days, 1 uL of 10 mM 181 was added to the drop with crystals. Within the first three minutes of 181 addition, the hOAT crystals turned their color from yellow to transparent. The crystals were soaked for 44 minutes, transferred into cryoprotective solution (well solution supplemented with 30% glycerol), and then flash-frozen in liquid nitrogen.
Resolution 2.10 Å R-free 0.235
7LON Ornithine Aminotransferase (OAT) cocrystallized with its inactivator - (1S,3S)-3-amino-4-(difluoromethylene)cyclohexene-1-carboxylic acid Deposited 2021-02-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 36–439（404 aa）
Not recorded THR THREONINE × 2 7QP (1R,3S,4R)-3-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]-4-methylcyclohexane-1-carboxylic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；The freshly prepared enzyme was buffer exchanged into 50 mM Tricine pH 7.8 and concentrated to a protein concentration of 6 mg/mL. For each hanging drop, 2 ul of protein solution was mixed with equal volume of well solution and 0.5 ul of 10 mM compound. The crystals with the best morphology and size grew in a final condition containing 12% PEG 6000, 200 mM NaCl, 10% glycerol, 50 mM Tricine pH 7.8.
Resolution 1.95 Å R-free 0.278
7LON Ornithine Aminotransferase (OAT) cocrystallized with its inactivator - (1S,3S)-3-amino-4-(difluoromethylene)cyclohexene-1-carboxylic acid Deposited 2021-02-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 36–439（404 aa）
Not recorded THR THREONINE × 2 7QP (1R,3S,4R)-3-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]-4-methylcyclohexane-1-carboxylic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；The freshly prepared enzyme was buffer exchanged into 50 mM Tricine pH 7.8 and concentrated to a protein concentration of 6 mg/mL. For each hanging drop, 2 ul of protein solution was mixed with equal volume of well solution and 0.5 ul of 10 mM compound. The crystals with the best morphology and size grew in a final condition containing 12% PEG 6000, 200 mM NaCl, 10% glycerol, 50 mM Tricine pH 7.8.
Resolution 1.95 Å R-free 0.278
7LON Ornithine Aminotransferase (OAT) cocrystallized with its inactivator - (1S,3S)-3-amino-4-(difluoromethylene)cyclohexene-1-carboxylic acid Deposited 2021-02-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 36–439（404 aa）
Not recorded THR THREONINE × 2 7QP (1R,3S,4R)-3-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]-4-methylcyclohexane-1-carboxylic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；The freshly prepared enzyme was buffer exchanged into 50 mM Tricine pH 7.8 and concentrated to a protein concentration of 6 mg/mL. For each hanging drop, 2 ul of protein solution was mixed with equal volume of well solution and 0.5 ul of 10 mM compound. The crystals with the best morphology and size grew in a final condition containing 12% PEG 6000, 200 mM NaCl, 10% glycerol, 50 mM Tricine pH 7.8.
Resolution 1.95 Å R-free 0.278
7T9Z Human Ornithine Aminotransferase (hOAT) crystallized at pH 6.0 Deposited 2021-12-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–439（439 aa）
Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；Purified holo-hOAT was buffer-exchanged into 100 mM MES, 200 mM NaCl, 100 uM PLP, pH 6.0 buffer, and then concentrated to ~6 mg/mL. The crystallization was performed via the hanging drop vapor diffusion method according to previously published conditions with 50 mM Tricine pH 7.8 substituted to 50 mM MES pH 6.0 buffer. The crystals grew at room temperature within three days and reached their maximum size in a week.
Resolution 2.15 Å R-free 0.276
7T9Z Human Ornithine Aminotransferase (hOAT) crystallized at pH 6.0 Deposited 2021-12-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–439（439 aa）
Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；Purified holo-hOAT was buffer-exchanged into 100 mM MES, 200 mM NaCl, 100 uM PLP, pH 6.0 buffer, and then concentrated to ~6 mg/mL. The crystallization was performed via the hanging drop vapor diffusion method according to previously published conditions with 50 mM Tricine pH 7.8 substituted to 50 mM MES pH 6.0 buffer. The crystals grew at room temperature within three days and reached their maximum size in a week.
Resolution 2.15 Å R-free 0.276
7T9Z Human Ornithine Aminotransferase (hOAT) crystallized at pH 6.0 Deposited 2021-12-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–439（439 aa）
Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；Purified holo-hOAT was buffer-exchanged into 100 mM MES, 200 mM NaCl, 100 uM PLP, pH 6.0 buffer, and then concentrated to ~6 mg/mL. The crystallization was performed via the hanging drop vapor diffusion method according to previously published conditions with 50 mM Tricine pH 7.8 substituted to 50 mM MES pH 6.0 buffer. The crystals grew at room temperature within three days and reached their maximum size in a week.
Resolution 2.15 Å R-free 0.276
7TA0 Human Ornithine Aminotransferase (hOAT) soaked with 5-aminovaleric acid Deposited 2021-12-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–439（439 aa）
Chain B 1–439（439 aa）
Not recorded I3B 5-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]pentanoic acid × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Once hOAT was purified, it was transferred to a 10 kDa centrifugal filter tube and concentrated to ~6 mg/mL. The holoenzyme crystals were first grown via a hanging drop vapor diffusion method. Each drop contained 2 uL of protein and 2 uL of well solution. The best crystallization condition contained 8% PEG 6000, 100 mM NaCl, 5% glycerol, and 50 mM Tricine pH 7.8. Once holoenzyme crystals reached their maximum size within seven days, 1 uL of 5-aminovaleric acid was added to the drop with crystals. The crystals were soaked for different time periods from 3 to 59 minutes. After soaking, crystals were transferred into a cryoprotective solution (well solution supplemented with 30% glycerol), and then flash-frozen in liquid nitrogen.
Resolution 2.33 Å R-free 0.236
7TA0 Human Ornithine Aminotransferase (hOAT) soaked with 5-aminovaleric acid Deposited 2021-12-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–439（439 aa）
Not recorded I3B 5-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]pentanoic acid × 2 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Once hOAT was purified, it was transferred to a 10 kDa centrifugal filter tube and concentrated to ~6 mg/mL. The holoenzyme crystals were first grown via a hanging drop vapor diffusion method. Each drop contained 2 uL of protein and 2 uL of well solution. The best crystallization condition contained 8% PEG 6000, 100 mM NaCl, 5% glycerol, and 50 mM Tricine pH 7.8. Once holoenzyme crystals reached their maximum size within seven days, 1 uL of 5-aminovaleric acid was added to the drop with crystals. The crystals were soaked for different time periods from 3 to 59 minutes. After soaking, crystals were transferred into a cryoprotective solution (well solution supplemented with 30% glycerol), and then flash-frozen in liquid nitrogen.
Resolution 2.33 Å R-free 0.236
7TA1 Human Ornithine Aminotransferase (hOAT) soaked with gamma-Aminobutyric acid Deposited 2021-12-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–439（439 aa）
Not recorded PLZ 4-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]BUTANOIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Once hOAT was purified, it was transferred to a 10 kDa centrifugal filter tube and concentrated to ~6 mg/mL. The holoenzyme crystals were first grown via a hanging drop vapor diffusion method. Each drop contained 2 uL of protein and 2 uL of well solution. The best crystallization condition contained 8% PEG 6000, 100 mM NaCl, 5% glycerol, and 50 mM Tricine pH 7.8. Once holoenzyme crystals reached their maximum size within seven days, 1 uL of 10 mM GABA was added to the drop with crystals. The crystals were soaked for different time periods from 50 minutes to 2.5 hours. After soaking, crystals were transferred into a cryoprotective solution (well solution supplemented with 30% glycerol), and then flash-frozen in liquid nitrogen.
Resolution 2.20 Å R-free 0.268
7TA1 Human Ornithine Aminotransferase (hOAT) soaked with gamma-Aminobutyric acid Deposited 2021-12-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–439（439 aa）
Not recorded PLZ 4-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]BUTANOIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Once hOAT was purified, it was transferred to a 10 kDa centrifugal filter tube and concentrated to ~6 mg/mL. The holoenzyme crystals were first grown via a hanging drop vapor diffusion method. Each drop contained 2 uL of protein and 2 uL of well solution. The best crystallization condition contained 8% PEG 6000, 100 mM NaCl, 5% glycerol, and 50 mM Tricine pH 7.8. Once holoenzyme crystals reached their maximum size within seven days, 1 uL of 10 mM GABA was added to the drop with crystals. The crystals were soaked for different time periods from 50 minutes to 2.5 hours. After soaking, crystals were transferred into a cryoprotective solution (well solution supplemented with 30% glycerol), and then flash-frozen in liquid nitrogen.
Resolution 2.20 Å R-free 0.268
7TA1 Human Ornithine Aminotransferase (hOAT) soaked with gamma-Aminobutyric acid Deposited 2021-12-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–439（439 aa）
Not recorded PLZ 4-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]BUTANOIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Once hOAT was purified, it was transferred to a 10 kDa centrifugal filter tube and concentrated to ~6 mg/mL. The holoenzyme crystals were first grown via a hanging drop vapor diffusion method. Each drop contained 2 uL of protein and 2 uL of well solution. The best crystallization condition contained 8% PEG 6000, 100 mM NaCl, 5% glycerol, and 50 mM Tricine pH 7.8. Once holoenzyme crystals reached their maximum size within seven days, 1 uL of 10 mM GABA was added to the drop with crystals. The crystals were soaked for different time periods from 50 minutes to 2.5 hours. After soaking, crystals were transferred into a cryoprotective solution (well solution supplemented with 30% glycerol), and then flash-frozen in liquid nitrogen.
Resolution 2.20 Å R-free 0.268
7TA1 Human Ornithine Aminotransferase (hOAT) soaked with gamma-Aminobutyric acid Deposited 2021-12-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–439（439 aa）
Not recorded PLZ 4-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]BUTANOIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Once hOAT was purified, it was transferred to a 10 kDa centrifugal filter tube and concentrated to ~6 mg/mL. The holoenzyme crystals were first grown via a hanging drop vapor diffusion method. Each drop contained 2 uL of protein and 2 uL of well solution. The best crystallization condition contained 8% PEG 6000, 100 mM NaCl, 5% glycerol, and 50 mM Tricine pH 7.8. Once holoenzyme crystals reached their maximum size within seven days, 1 uL of 10 mM GABA was added to the drop with crystals. The crystals were soaked for different time periods from 50 minutes to 2.5 hours. After soaking, crystals were transferred into a cryoprotective solution (well solution supplemented with 30% glycerol), and then flash-frozen in liquid nitrogen.
Resolution 2.20 Å R-free 0.268
7TA1 Human Ornithine Aminotransferase (hOAT) soaked with gamma-Aminobutyric acid Deposited 2021-12-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 1–439（439 aa）
Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Once hOAT was purified, it was transferred to a 10 kDa centrifugal filter tube and concentrated to ~6 mg/mL. The holoenzyme crystals were first grown via a hanging drop vapor diffusion method. Each drop contained 2 uL of protein and 2 uL of well solution. The best crystallization condition contained 8% PEG 6000, 100 mM NaCl, 5% glycerol, and 50 mM Tricine pH 7.8. Once holoenzyme crystals reached their maximum size within seven days, 1 uL of 10 mM GABA was added to the drop with crystals. The crystals were soaked for different time periods from 50 minutes to 2.5 hours. After soaking, crystals were transferred into a cryoprotective solution (well solution supplemented with 30% glycerol), and then flash-frozen in liquid nitrogen.
Resolution 2.20 Å R-free 0.268
7TA1 Human Ornithine Aminotransferase (hOAT) soaked with gamma-Aminobutyric acid Deposited 2021-12-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain F 1–439（439 aa）
Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Once hOAT was purified, it was transferred to a 10 kDa centrifugal filter tube and concentrated to ~6 mg/mL. The holoenzyme crystals were first grown via a hanging drop vapor diffusion method. Each drop contained 2 uL of protein and 2 uL of well solution. The best crystallization condition contained 8% PEG 6000, 100 mM NaCl, 5% glycerol, and 50 mM Tricine pH 7.8. Once holoenzyme crystals reached their maximum size within seven days, 1 uL of 10 mM GABA was added to the drop with crystals. The crystals were soaked for different time periods from 50 minutes to 2.5 hours. After soaking, crystals were transferred into a cryoprotective solution (well solution supplemented with 30% glycerol), and then flash-frozen in liquid nitrogen.
Resolution 2.20 Å R-free 0.268
7TED Human Ornithine Aminotransferase cocrystallized with its inhibitor, (S,E)-3-amino-4-(fluoromethylene)cyclopent-1-ene-1-carboxylate Deposited 2022-01-04 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 36–439（404 aa）
Chain B 36–439（404 aa）
Not recorded I1T (1S,3R,4S)-3-formyl-4-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]cyclopentane-1-carboxylic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；After purification, OAT was buffer exchanged into the crystallization buffer (50 mM Tricine pH 7.8) supplied supplemented with 1 mM 2-ketoglutarate. The protein was concentrated to 6.5 mg/mL. Previously reported crystallization conditions were optimized using the hanging drop vapor diffusion method by varying PEG 6000 (8-12%), NaCl (100-250 mM), and glycerol (0%-10%) with 100 mM Tricine pH 7.8 was being kept constant as the buffer. For each hanging drop, 2 uL of protein solution was mixed with an equal volume of well solution and 0.5 uL of ligand. The crystals with the best morphology and size grew in a final condition containing 12% PEG 6000, 200 mM NaCl, 10% glycerol, and 100 mM Tricine pH 7.8. Crystals were transferred to a cryo-protectant solution (well solution supplemented with 30% glycerol) and flash-frozen in liquid nitrogen
Resolution 2.63 Å R-free 0.288
7TED Human Ornithine Aminotransferase cocrystallized with its inhibitor, (S,E)-3-amino-4-(fluoromethylene)cyclopent-1-ene-1-carboxylate Deposited 2022-01-04 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 36–439（404 aa）
Chain I 36–439（404 aa）
Not recorded I1T (1S,3R,4S)-3-formyl-4-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]cyclopentane-1-carboxylic acid × 1 PLP PYRIDOXAL-5'-PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；After purification, OAT was buffer exchanged into the crystallization buffer (50 mM Tricine pH 7.8) supplied supplemented with 1 mM 2-ketoglutarate. The protein was concentrated to 6.5 mg/mL. Previously reported crystallization conditions were optimized using the hanging drop vapor diffusion method by varying PEG 6000 (8-12%), NaCl (100-250 mM), and glycerol (0%-10%) with 100 mM Tricine pH 7.8 was being kept constant as the buffer. For each hanging drop, 2 uL of protein solution was mixed with an equal volume of well solution and 0.5 uL of ligand. The crystals with the best morphology and size grew in a final condition containing 12% PEG 6000, 200 mM NaCl, 10% glycerol, and 100 mM Tricine pH 7.8. Crystals were transferred to a cryo-protectant solution (well solution supplemented with 30% glycerol) and flash-frozen in liquid nitrogen
Resolution 2.63 Å R-free 0.288
7TED Human Ornithine Aminotransferase cocrystallized with its inhibitor, (S,E)-3-amino-4-(fluoromethylene)cyclopent-1-ene-1-carboxylate Deposited 2022-01-04 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain D 36–439（404 aa）
Chain E 36–439（404 aa）
Not recorded I1T (1S,3R,4S)-3-formyl-4-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]cyclopentane-1-carboxylic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；After purification, OAT was buffer exchanged into the crystallization buffer (50 mM Tricine pH 7.8) supplied supplemented with 1 mM 2-ketoglutarate. The protein was concentrated to 6.5 mg/mL. Previously reported crystallization conditions were optimized using the hanging drop vapor diffusion method by varying PEG 6000 (8-12%), NaCl (100-250 mM), and glycerol (0%-10%) with 100 mM Tricine pH 7.8 was being kept constant as the buffer. For each hanging drop, 2 uL of protein solution was mixed with an equal volume of well solution and 0.5 uL of ligand. The crystals with the best morphology and size grew in a final condition containing 12% PEG 6000, 200 mM NaCl, 10% glycerol, and 100 mM Tricine pH 7.8. Crystals were transferred to a cryo-protectant solution (well solution supplemented with 30% glycerol) and flash-frozen in liquid nitrogen
Resolution 2.63 Å R-free 0.288
7TED Human Ornithine Aminotransferase cocrystallized with its inhibitor, (S,E)-3-amino-4-(fluoromethylene)cyclopent-1-ene-1-carboxylate Deposited 2022-01-04 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain F 36–439（404 aa）
Not recorded I1T (1S,3R,4S)-3-formyl-4-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]cyclopentane-1-carboxylic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；After purification, OAT was buffer exchanged into the crystallization buffer (50 mM Tricine pH 7.8) supplied supplemented with 1 mM 2-ketoglutarate. The protein was concentrated to 6.5 mg/mL. Previously reported crystallization conditions were optimized using the hanging drop vapor diffusion method by varying PEG 6000 (8-12%), NaCl (100-250 mM), and glycerol (0%-10%) with 100 mM Tricine pH 7.8 was being kept constant as the buffer. For each hanging drop, 2 uL of protein solution was mixed with an equal volume of well solution and 0.5 uL of ligand. The crystals with the best morphology and size grew in a final condition containing 12% PEG 6000, 200 mM NaCl, 10% glycerol, and 100 mM Tricine pH 7.8. Crystals were transferred to a cryo-protectant solution (well solution supplemented with 30% glycerol) and flash-frozen in liquid nitrogen
Resolution 2.63 Å R-free 0.288
7TED Human Ornithine Aminotransferase cocrystallized with its inhibitor, (S,E)-3-amino-4-(fluoromethylene)cyclopent-1-ene-1-carboxylate Deposited 2022-01-04 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain G 36–439（404 aa）
Chain H 36–439（404 aa）
Not recorded I1T (1S,3R,4S)-3-formyl-4-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]cyclopentane-1-carboxylic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；After purification, OAT was buffer exchanged into the crystallization buffer (50 mM Tricine pH 7.8) supplied supplemented with 1 mM 2-ketoglutarate. The protein was concentrated to 6.5 mg/mL. Previously reported crystallization conditions were optimized using the hanging drop vapor diffusion method by varying PEG 6000 (8-12%), NaCl (100-250 mM), and glycerol (0%-10%) with 100 mM Tricine pH 7.8 was being kept constant as the buffer. For each hanging drop, 2 uL of protein solution was mixed with an equal volume of well solution and 0.5 uL of ligand. The crystals with the best morphology and size grew in a final condition containing 12% PEG 6000, 200 mM NaCl, 10% glycerol, and 100 mM Tricine pH 7.8. Crystals were transferred to a cryo-protectant solution (well solution supplemented with 30% glycerol) and flash-frozen in liquid nitrogen
Resolution 2.63 Å R-free 0.288
7TEV Human Ornithine Aminotransferase cocrystallized with its inhibitor, (3S,4R)-3-amino-4-(difluoromethyl)cyclopent-1-ene-1-carboxylate Deposited 2022-01-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 36–439（404 aa）
Not recorded I1T (1S,3R,4S)-3-formyl-4-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]cyclopentane-1-carboxylic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；After purification, hOAT was buffer exchanged into the crystallization buffer (50 mM Tricine pH 7.8) supplemented with 1 mM 2-ketoglutarate. The protein was concentrated to 6.5 mg/mL. Previously reported crystallization conditions were optimized using the hanging drop vapor diffusion method by varying PEG 6000 (8-12%), NaCl (100-250 mM), and glycerol (0%-10%) with 100 mM Tricine pH 7.8 being kept constant as the buffer. For each hanging drop, 2 uL of protein solution was mixed with an equal volume of well solution and 0.5 uL of ligand. The crystals with the best morphology and size grew in a final condition containing 12% PEG 6000, 200 mM NaCl, 10% glycerol, and 100 mM Tricine pH 7.8. Crystals were transferred to a cryo-protectant solution (well solution supplemented with 30% glycerol) and flash-frozen in liquid nitrogen.
Resolution 1.91 Å R-free 0.269
7TEV Human Ornithine Aminotransferase cocrystallized with its inhibitor, (3S,4R)-3-amino-4-(difluoromethyl)cyclopent-1-ene-1-carboxylate Deposited 2022-01-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 36–439（404 aa）
Chain C 36–439（404 aa）
Not recorded I1T (1S,3R,4S)-3-formyl-4-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]cyclopentane-1-carboxylic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；After purification, hOAT was buffer exchanged into the crystallization buffer (50 mM Tricine pH 7.8) supplemented with 1 mM 2-ketoglutarate. The protein was concentrated to 6.5 mg/mL. Previously reported crystallization conditions were optimized using the hanging drop vapor diffusion method by varying PEG 6000 (8-12%), NaCl (100-250 mM), and glycerol (0%-10%) with 100 mM Tricine pH 7.8 being kept constant as the buffer. For each hanging drop, 2 uL of protein solution was mixed with an equal volume of well solution and 0.5 uL of ligand. The crystals with the best morphology and size grew in a final condition containing 12% PEG 6000, 200 mM NaCl, 10% glycerol, and 100 mM Tricine pH 7.8. Crystals were transferred to a cryo-protectant solution (well solution supplemented with 30% glycerol) and flash-frozen in liquid nitrogen.
Resolution 1.91 Å R-free 0.269
7TFP Human Ornithine Aminotransferase cocrystallized with its inhibitor, (1S,3S)-3-amino-4-(difluoromethylene)cyclopentane-1-carboxylic acid. Deposited 2022-01-06 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 36–439（404 aa）
Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；After purification, hOAT was buffer exchanged into the crystallization buffer (50 mM Tricine pH 7.8) supplemented with 1 mM 2-ketoglutarate. The protein was concentrated to 6.5 mg/mL. Previously reported crystallization conditions were optimized using the hanging drop vapor diffusion method by varying PEG 6000 (8-12%), NaCl (100-250 mM), and glycerol (0%-10%) with 100 mM Tricine pH 7.8 being kept constant as the buffer. For each hanging drop, 2 uL of protein solution was mixed with an equal volume of well solution and 0.5 uL of ligand. The crystals with the best morphology and size grew in a final condition containing 12% PEG 6000, 200 mM NaCl, 10% glycerol, and 100 mM Tricine pH 7.8. Crystals were transferred to a cryo-protectant solution (well solution supplemented with 30% glycerol) and flash-frozen in liquid nitrogen.
Resolution 2.71 Å R-free 0.268
7TFP Human Ornithine Aminotransferase cocrystallized with its inhibitor, (1S,3S)-3-amino-4-(difluoromethylene)cyclopentane-1-carboxylic acid. Deposited 2022-01-06 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 36–439（404 aa）
Chain C 36–439（404 aa）
Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 2 I2V (1S,3S,4S)-3-amino-4-(fluoromethyl)cyclopentane-1-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；After purification, hOAT was buffer exchanged into the crystallization buffer (50 mM Tricine pH 7.8) supplemented with 1 mM 2-ketoglutarate. The protein was concentrated to 6.5 mg/mL. Previously reported crystallization conditions were optimized using the hanging drop vapor diffusion method by varying PEG 6000 (8-12%), NaCl (100-250 mM), and glycerol (0%-10%) with 100 mM Tricine pH 7.8 being kept constant as the buffer. For each hanging drop, 2 uL of protein solution was mixed with an equal volume of well solution and 0.5 uL of ligand. The crystals with the best morphology and size grew in a final condition containing 12% PEG 6000, 200 mM NaCl, 10% glycerol, and 100 mM Tricine pH 7.8. Crystals were transferred to a cryo-protectant solution (well solution supplemented with 30% glycerol) and flash-frozen in liquid nitrogen.
Resolution 2.71 Å R-free 0.268
8EZ1 Human Ornithine Aminotransferase (hOAT) co-crystallized with its inactivator 3-Amino-4-fluorocyclopentenecarboxylic Acid Deposited 2022-10-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 36–439（404 aa）
Chain B 36–439（404 aa）
Not recorded X8B (3E,4E)-4-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-3-iminocyclopent-1-ene-1-carboxylic acid × 1 X8H (1R,3S,4Z)-3-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-4-iminocyclopentane-1-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；The crystals with the best morphology and size grew in a final condition containing 10% PEG 6000, 100 mM NaCl, 10% glycerol, 100 mM Tricine pH 7.8.
Resolution 1.91 Å R-free 0.237
8EZ1 Human Ornithine Aminotransferase (hOAT) co-crystallized with its inactivator 3-Amino-4-fluorocyclopentenecarboxylic Acid Deposited 2022-10-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 36–439（404 aa）
Not recorded X8B (3E,4E)-4-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-3-iminocyclopent-1-ene-1-carboxylic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；The crystals with the best morphology and size grew in a final condition containing 10% PEG 6000, 100 mM NaCl, 10% glycerol, 100 mM Tricine pH 7.8.
Resolution 1.91 Å R-free 0.237
8V9M Human Ornithine Aminotransferase cocrystallized with its inhibitor, (R)-3-amino-5,5-difluorocyclohex-1-ene-1-carboxylic acid. Deposited 2023-12-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 36–439（404 aa）
Not recorded YR5 3-fluoro-5-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]benzoic acid × 2 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；298 K；10% PEG 6000, 100 mM NaCl, 20% glycerol, 100 mM tricine, pH 7.8
Resolution 1.61 Å R-free 0.193
8V9M Human Ornithine Aminotransferase cocrystallized with its inhibitor, (R)-3-amino-5,5-difluorocyclohex-1-ene-1-carboxylic acid. Deposited 2023-12-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 36–439（404 aa）
Chain C 36–439（404 aa）
Not recorded YR5 3-fluoro-5-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]benzoic acid × 2 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；298 K；10% PEG 6000, 100 mM NaCl, 20% glycerol, 100 mM tricine, pH 7.8
Resolution 1.61 Å R-free 0.193

26 other PDB entries and 65 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name OAT_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–402； UniProt 38–439 Author chain B； PDBConstruct 1–402； UniProt 38–439 Author chain C； PDBConstruct 1–402； UniProt 38–439

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1gbn

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1gbn
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1gbn
Deposition date deposition_date1997-05-29
Structure title titleHUMAN ORNITHINE AMINOTRANSFERASE COMPLEXED WITH THE NEUROTOXIN GABACULINE
Keywords keywords;TRANSFERASE, ORNITHINE AMINOTRANSFERASE, UREA CYCLE, PYRIDOXAL-5'-PHOSPHATE ;; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier34.76 Å
Radius of gyration Rg (electron density) rg_electron34.45 Å
Forward intensity I(0) i0263449000.00
Molecular weight molecular_weight135060.0 kDa
Excluded volume excluded_volume170650 ų
Envelope volume envelope_volume203460 ų
Hydration-shell volume shell_volume49440 ų
Envelope diameter envelope_diameter119.6 Å
Shell Rg shell_rg40.84 Å
Envelope Rg envelope_rg34.47 Å
Shape Rg shape_rg34.44 Å
Total Rg total_rg34.91 Å
Total atoms total_atoms11559
Residues n_residues1206
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax117.0 Å
Rg (real space) rg_real34.84 Å
Rg uncertainty (real space) rg_real_error0.68 Å
I(0) (real space) i0_real2.6340e+08
I(0) uncertainty (real space) i0_real_error3.5730e+06
Rg (reciprocal space) rg_reciprocal34.79 Å
I(0) (reciprocal space) i0_reciprocal263400000.0000
Solution quality estimate total_estimate0.6371
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary38.1 Å
Skewness Skewness skewness0.460
Kurtosis Kurtosis kurtosis-0.241
Angular range angular_range— – 0.2300 Å−1
Current regularization parameter α current_alpha0.0002
Highest regularization parameter α highest_alpha80760000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.819; Stabil: 1.000; Sysdev: 0.009; Positv: 1.000; Valcen: 0.992; Smooth: 0.804
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1gbna_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamilyc.67.1 — PLP-dependent transferases
Family Family familyc.67.1.4 — GABA-aminotransferase-like
Domain ID domain_idd1gbnb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamilyc.67.1 — PLP-dependent transferases
Family Family familyc.67.1.4 — GABA-aminotransferase-like
Domain ID domain_idd1gbnc_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamilyc.67.1 — PLP-dependent transferases
Family Family familyc.67.1.4 — GABA-aminotransferase-like

CATH v4.4 (6 domains)

Domain ID domain_id1gbnA01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily10 — Aspartate Aminotransferase, domain 1
Domain ID domain_id1gbnA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)
Domain ID domain_id1gbnB01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily10 — Aspartate Aminotransferase, domain 1
Domain ID domain_id1gbnB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)
Domain ID domain_id1gbnC01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily10 — Aspartate Aminotransferase, domain 1
Domain ID domain_id1gbnC02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)
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8. Citations (1)

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9. Files and Curves (10)