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

Ornithine Aminotransferase (OAT) soaked with its inactivator - (1S,3S)-3-amino-4-(difluoromethylene)cyclohexene-1-carboxylic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x THR: THREONINE(Covalent)

THR.1: 7 residues within 4Å: Chain A: S.49, K.257 Chain B: L.75, S.286, Y.288, G.289 Ligands: Y8P.2 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.286, B:G.289 Water bridges: B:R.78, B:Y.288 THR.3: 5 residues within 4Å: Chain A: L.75, S.286, Y.288, G.289 Ligands: YCD.4 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.286 Water bridges: A:N.105, A:N.105, A:G.285, A:S.286, A:S.286, A:S.286, B:Y.20

1 x Y8P: (3~{S},4~{S})-4-methyl-3-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]cyclohexene-1-carboxylic acid(Covalent)

Y8P.2: 15 residues within 4Å: Chain A: Y.50, T.106, G.107, V.108, F.142, W.143, G.144, E.195, E.200, D.228, I.230, Q.231, K.257, R.378 Ligands: THR.1 16 PLIP interactions: 11 interactions with chain A, 2 interactions with chain B, 3 Ligand-Ligand interactions Hydrophobic interactions: A:Y.50, A:E.195, A:K.257, T.1 Hydrogen bonds: A:G.107, A:V.108, A:Q.231, T.1, T.1 Water bridges: A:T.106, A:T.106, B:G.285, B:Y.288 Salt bridges: A:K.257, A:R.378 pi-Stacking: A:Y.50

1 x YCD: (4~{R})-4-(fluoranylmethyl)-3-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]cyclohexene-1-carboxylic acid(Non-covalent)

YCD.4: 15 residues within 4Å: Chain B: Y.50, T.106, G.107, V.108, F.142, W.143, G.144, E.195, E.200, D.228, I.230, Q.231, K.257, R.378 Ligands: THR.3 17 PLIP interactions: 13 interactions with chain B, 1 interactions with chain A, 3 Ligand-Ligand interactions Hydrophobic interactions: B:Y.50 Hydrogen bonds: B:T.106, B:T.106, B:G.107, B:V.108, B:Q.231, B:Q.231, B:K.257, B:K.257, T.3 Water bridges: B:Y.50, A:N.105, T.3, T.3 Salt bridges: B:R.378 pi-Stacking: B:Y.50, B:F.142

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, W. et al., Remarkable and Unexpected Mechanism for ( S )-3-Amino-4-(difluoromethylenyl)cyclohex-1-ene-1-carboxylic Acid as a Selective Inactivator of Human Ornithine Aminotransferase. J.Am.Chem.Soc. (2021)

Release Date

2021-08-25

Peptides

Ornithine aminotransferase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

Ornithine aminotransferase, mitochondrial

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