SMTL ID : 4bmk.1

Serine Palmitoyltransferase K265A from S. paucimobilis with bound PLP- Myriocin Aldimine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PLP.1: 16 residues within 4Å: Chain A: T.154, G.155, Y.156, N.159, H.180, S.182, E.223, S.227, D.252, H.255, T.283, S.285, G.292 Chain B: T.315, A.316 Ligands: MYB.2 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:H.180 Hydrogen bonds: A:G.155, A:Y.156, A:N.159, A:S.227, A:S.227, A:T.283, A:S.285, A:G.292, B:T.315, B:A.316 pi-Stacking: A:H.180 PLP.5: 15 residues within 4Å: Chain A: T.315, A.316 Chain B: T.154, G.155, Y.156, N.159, H.180, E.223, S.227, D.252, H.255, T.283, S.285, G.292 Ligands: MYB.6 13 PLIP interactions: 3 interactions with chain A, 10 interactions with chain B Hydrogen bonds: A:T.315, A:T.315, A:A.316, B:G.155, B:Y.156, B:N.159, B:S.227, B:S.227, B:T.283, B:S.285, B:G.292 Hydrophobic interactions: B:H.180 pi-Stacking: B:H.180

2 x MYB: Decarboxylated Myriocin(Non-covalent)

MYB.2: 9 residues within 4Å: Chain A: Y.94, H.180, A.402 Chain B: L.126, I.313, F.314, T.315, A.316 Ligands: PLP.1 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Y.94, A:Y.94, B:F.314, B:T.315 Hydrophobic interactions: B:L.126, B:F.314 MYB.6: 8 residues within 4Å: Chain A: L.126, I.313, F.314, T.315, A.316 Chain B: Y.94, H.180 Ligands: PLP.5 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.313, A:F.314, A:F.314 Hydrogen bonds: A:F.314, A:T.315

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: T.363, E.364, T.365, D.367 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.364, A:T.365, A:D.367 GOL.4: 3 residues within 4Å: Chain A: R.340, E.341, W.344 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.340, A:E.341 Water bridges: A:G.261

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wadsworth, J.M. et al., The Chemical Basis of Serine Palmitoyltransferase Inhibition by Myriocin. J.Am.Chem.Soc. (2013)

Release Date

2013-09-04

Peptides

SERINE PALMITOYLTRANSFERASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

SERINE PALMITOYLTRANSFERASE