SMTL ID : 3a2b.1

Crystal Structure of Serine Palmitoyltransferase from Sphingobacterium multivorum with substrate L-serine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x SER: SERINE(Non-covalent)

SER.1: 10 residues within 4Å: Chain A: N.51, H.137, S.242, K.243 Chain B: S.80, M.270, F.271, S.272, A.273 Ligands: PLP.2 13 PLIP interactions: 8 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:N.51, A:S.242, A:S.242, A:K.243, B:S.80, B:A.273 Water bridges: A:S.184, A:S.184, A:S.184, B:S.80, B:S.80, B:S.80 Salt bridges: A:H.137 SER.3: 10 residues within 4Å: Chain A: S.80, M.270, F.271, S.272, A.273 Chain B: N.51, H.137, S.242, K.243 Ligands: PLP.4 13 PLIP interactions: 8 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:N.51, B:S.242, B:S.242, B:K.243, A:S.80, A:A.273 Water bridges: B:S.184, B:S.184, B:S.184, A:S.80, A:S.80, A:S.80 Salt bridges: B:H.137

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

PLP.2: 18 residues within 4Å: Chain A: T.111, G.112, F.113, N.116, H.137, S.139, D.180, D.209, A.211, H.212, M.238, T.240, S.242, K.243 Chain B: F.271, S.272, A.273 Ligands: SER.1 16 PLIP interactions: 13 interactions with chain A, 2 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: A:H.137, A:A.211, A:T.240 Hydrogen bonds: A:G.112, A:F.113, A:N.116, A:S.139, A:H.212, A:S.242, A:S.242, B:S.272, B:A.273, S.1 Water bridges: A:S.184 Salt bridges: A:K.243 pi-Stacking: A:H.137 PLP.4: 18 residues within 4Å: Chain A: F.271, S.272, A.273 Chain B: T.111, G.112, F.113, N.116, H.137, S.139, D.180, D.209, A.211, H.212, M.238, T.240, S.242, K.243 Ligands: SER.3 16 PLIP interactions: 13 interactions with chain B, 2 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: B:H.137, B:A.211, B:T.240 Hydrogen bonds: B:G.112, B:F.113, B:N.116, B:S.139, B:H.212, B:S.242, B:S.242, A:S.272, A:A.273, S.3 Water bridges: B:S.184 Salt bridges: B:K.243 pi-Stacking: B:H.137

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ikushiro, H. et al., Structural Insights into the Enzymatic Mechanism of Serine Palmitoyltransferase from Sphingobacterium multivorum. J.Biochem. (2009)

Release Date

2009-07-14

Peptides

Serine palmitoyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Serine palmitoyltransferase