SMTL ID : 7jx9.1 (1 other biounit)

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.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

homo-dimer

Ligands

2 x 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(Non-covalent)

IF1.1: 17 residues within 4Å: Chain A: Y.20, 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 Chain B: S.286, T.287 20 PLIP interactions: 14 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:Y.50, A:Y.50, A:Y.50, A:F.142, A:F.142 Hydrogen bonds: A:G.107, A:V.108, A:Q.231, A:K.257, B:S.286, B:T.287, B:T.287, B:T.287 Water bridges: A:T.106, A:T.106, A:R.145, B:G.285, B:Y.288 Halogen bonds: A:K.257, A:R.378 IF1.3: 17 residues within 4Å: Chain A: S.286, T.287 Chain B: Y.20, 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 20 PLIP interactions: 14 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:Y.50, B:Y.50, B:Y.50, B:F.142, B:F.142 Hydrogen bonds: B:Y.20, B:T.106, B:G.107, B:V.108, B:Q.231, B:K.257, A:S.286, A:T.287, A:T.287, A:T.287 Water bridges: B:R.145, A:G.285, A:Y.288 Halogen bonds: B:K.257, B:R.378

2 x VLS: N-[1,3-dihydroxy-2-(hydroxymethyl)propan-2-yl]glycine(Non-covalent)

VLS.2: 6 residues within 4Å: Chain A: S.151, F.165, M.166, P.167, G.168, F.169 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.169 Water bridges: A:G.168, A:I.171 VLS.4: 6 residues within 4Å: Chain B: S.151, F.165, M.166, P.167, G.168, F.169 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.169 Water bridges: B:G.168, B:I.171

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Butrin, A. et al., Structural and Kinetic Analyses Reveal the Dual Inhibition Modes of Ornithine Aminotransferase by (1 S ,3 S )-3-Amino-4-(hexafluoropropan-2-ylidenyl)-cyclopentane-1-carboxylic Acid (BCF 3 ). Acs Chem.Biol. (2021)

Release Date

2021-01-06

Peptides

Ornithine aminotransferase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Ornithine aminotransferase, mitochondrial

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