SMTL ID : 5wp4.1

Arabidopsis thaliana phosphoethanolamine N-methyltransferase 1 (AtPMT1, XIOPTL) in complex with SAH and phosphocholine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.34 Å

Oligo State

monomer

Ligands

2 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.1: 20 residues within 4Å: Chain A: R.9, W.16, M.28, G.61, A.62, G.63, R.66, F.67, L.81, D.82, F.83, I.84, A.106, D.107, V.108, N.126, W.127, L.128, L.132 Ligands: PC.4 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:R.9, A:G.63, A:F.83, A:D.107, A:V.108, A:N.126, A:N.126, A:N.126 Water bridges: A:R.9, A:S.20, A:A.62 Salt bridges: A:R.66 pi-Stacking: A:F.83, A:F.83 SAH.3: 22 residues within 4Å: Chain A: F.237, L.241, Y.246, F.262, V.263, S.264, G.290, C.291, G.292, D.312, L.313, S.314, M.317, A.337, D.338, C.339, R.355, D.356, T.357, H.360, I.361 Ligands: PC.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:V.263, A:L.313, A:S.314, A:D.338, A:D.338, A:C.339, A:R.355, A:T.357 Water bridges: A:C.291, A:T.340, A:R.355

2 x PC: PHOSPHOCHOLINE(Non-covalent)

PC.2: 13 residues within 4Å: Chain A: Q.245, Y.246, Y.254, V.263, S.264, D.356, L.359, Y.386, Y.400, R.404, Y.406, K.472 Ligands: SAH.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.245, A:Y.254, A:Y.386, A:Y.406 Water bridges: A:R.404, A:G.468 Salt bridges: A:R.404, A:K.472 PC.4: 14 residues within 4Å: Chain A: W.16, M.28, M.29, L.30, W.127, M.130, Y.131, S.159, Q.163, S.164, G.165, R.169, Y.176 Ligands: SAH.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.159, A:S.164, A:G.165, A:Y.176, A:Y.176 Water bridges: A:Y.15, A:R.169 Salt bridges: A:R.169 pi-Cation interactions: A:W.127, A:W.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, S.G. et al., Conformational changes in the di-domain structure of Arabidopsis phosphoethanolamine methyltransferase leads to active-site formation. J. Biol. Chem. (2017)

Release Date

2017-11-15

Peptides

Phosphoethanolamine N-methyltransferase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Phosphoethanolamine N-methyltransferase 1