SMTL ID : 7tfp.2 (1 other biounit)

Human Ornithine Aminotransferase cocrystallized with its inhibitor, (1S,3S)-3-amino-4-(difluoromethylene)cyclopentane-1-carboxylic acid.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.71 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.1: 12 residues within 4Å: Chain A: T.106, G.107, V.108, F.142, W.143, E.195, D.228, I.230, Q.231, K.257 Chain B: S.286, T.287 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:F.142, A:K.257 Hydrogen bonds: A:V.108, A:E.200, A:Q.231, A:K.257, B:T.287, B:T.287 Salt bridges: A:K.257 Water bridges: B:T.287, B:Y.288 PLP.2: 13 residues within 4Å: Chain A: E.109, S.286, T.287 Chain B: T.106, G.107, V.108, F.142, W.143, D.228, I.230, Q.231, K.257 Ligands: I2V.3 14 PLIP interactions: 4 interactions with chain A, 10 interactions with chain B Hydrogen bonds: A:T.287, A:T.287, A:T.287, B:T.106, B:G.107, B:V.108, B:Q.231, B:Q.231, B:K.257 Water bridges: A:Y.288, B:I.230 Hydrophobic interactions: B:D.228, B:I.230, B:K.257

1 x I2V: (1S,3S,4S)-3-amino-4-(fluoromethyl)cyclopentane-1-carboxylic acid(Non-covalent)

I2V.3: 10 residues within 4Å: Chain A: S.286, T.287 Chain B: Y.20, Y.50, F.142, E.200, Q.231, K.257, R.378 Ligands: PLP.2 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.50, B:Y.50, B:Y.50, B:F.142 Hydrogen bonds: B:Y.20, A:S.286 Water bridges: B:Y.20, A:S.286

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, W. et al., Rational Design, Synthesis, and Mechanism of (3 S ,4 R )-3-Amino-4-(difluoromethyl)cyclopent-1-ene-1-carboxylic Acid: Employing a Second-Deprotonation Strategy for Selectivity of Human Ornithine Aminotransferase over GABA Aminotransferase. J.Am.Chem.Soc. (2022)

Release Date

2022-04-06

Peptides

Ornithine aminotransferase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

Ornithine aminotransferase, mitochondrial

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