Ornithine aminotransferase, mitochondrial
Homo sapiens
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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count | Chain A； UniProt 36–439 Chain B； UniProt 36–439 | 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 |
| 2 | Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count | Chain C； UniProt 36–439 Chain I； UniProt 36–439 | 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 |
| 3 | Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count | Chain D； UniProt 36–439 Chain E； UniProt 36–439 | 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 |
| 4 | Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count | Chain F； UniProt 36–439 | 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 |
| 5 | Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count | Chain G； UniProt 36–439 Chain H； UniProt 36–439 | 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 |
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 7TED | 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 |
| 1GBN HUMAN ORNITHINE AMINOTRANSFERASE COMPLEXED WITH THE NEUROTOXIN GABACULINE Deposited 1997-05-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
38–439（402 aa）
Chain B
38–439（402 aa）
Chain C
38–439（402 aa）
|
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 |
| 1GBN HUMAN ORNITHINE AMINOTRANSFERASE COMPLEXED WITH THE NEUROTOXIN GABACULINE Deposited 1997-05-29 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
38–439（402 aa）
Chain B
38–439（402 aa）
|
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 |
| 1GBN HUMAN ORNITHINE AMINOTRANSFERASE COMPLEXED WITH THE NEUROTOXIN GABACULINE Deposited 1997-05-29 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain C
38–439（402 aa）
|
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 |
| 1GBN HUMAN ORNITHINE AMINOTRANSFERASE COMPLEXED WITH THE NEUROTOXIN GABACULINE Deposited 1997-05-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
38–439（402 aa）
Chain B
38–439（402 aa）
Chain C
38–439（402 aa）
|
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 |
| 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 construct Different ligand/ion Different experimental conditions 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 construct Different ligand/ion Different experimental conditions 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 |
| 7TEV Human Ornithine Aminotransferase cocrystallized with its inhibitor, (3S,4R)-3-amino-4-(difluoromethyl)cyclopent-1-ene-1-carboxylate Deposited 2022-01-05 | 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 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 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 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 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 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 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 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 64 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 1–404； UniProt 36–439 Author chain B； PDBConstruct 1–404； UniProt 36–439 Author chain C； PDBConstruct 1–404； UniProt 36–439 Author chain D； PDBConstruct 1–404； UniProt 36–439 Author chain E； PDBConstruct 1–404； UniProt 36–439 Author chain F； PDBConstruct 1–404； UniProt 36–439 Author chain G； PDBConstruct 1–404； UniProt 36–439 Author chain H； PDBConstruct 1–404； UniProt 36–439 Author chain I； PDBConstruct 1–404； UniProt 36–439 |
