SMTL ID : 8h20.1

Serine Palmitoyltransferase from Sphingobacterium multivorum complexed with Glycine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

2 x PLG: N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE](Non-covalent)

PLG.1: 19 residues within 4Å: Chain A: T.112, G.113, F.114, N.117, H.138, S.140, D.181, D.210, A.212, H.213, M.239, T.241, S.243, K.244 Chain B: S.81, M.271, F.272, S.273, A.274 18 PLIP interactions: 3 interactions with chain B, 15 interactions with chain A Hydrogen bonds: B:S.81, B:S.81, B:A.274, A:G.113, A:F.114, A:N.117, A:H.213, A:S.243, A:S.243, A:K.244, A:K.244 Hydrophobic interactions: A:H.138, A:A.212 Water bridges: A:T.241, A:T.241 Salt bridges: A:H.138, A:K.244 pi-Stacking: A:H.138 PLG.10: 19 residues within 4Å: Chain A: S.81, M.271, F.272, S.273, A.274 Chain B: T.112, G.113, F.114, N.117, H.138, S.140, D.181, D.210, A.212, H.213, M.239, T.241, S.243, K.244 17 PLIP interactions: 14 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:H.138, B:A.212 Hydrogen bonds: B:G.113, B:F.114, B:N.117, B:H.213, B:T.241, B:S.243, B:S.243, B:K.244, B:K.244, A:S.81, A:S.81, A:A.274 Salt bridges: B:H.138, B:K.244 pi-Stacking: B:H.138

16 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 2 residues within 4Å: Chain A: D.314, H.315 Ligand excluded by PLIP EDO.3: 6 residues within 4Å: Chain A: D.233, D.234, V.235, D.236 Chain B: S.2, K.3 Ligand excluded by PLIP EDO.4: 2 residues within 4Å: Chain A: E.38, R.45 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: I.15, E.18, L.19, K.22, E.335 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: H.315, G.316, F.317, F.390 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: R.62, K.286, E.289, I.290, N.293 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: I.15, Y.27, F.338, V.355 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: K.22, L.24, W.339, M.343 Ligand excluded by PLIP EDO.11: 2 residues within 4Å: Chain B: D.314, H.315 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: S.2, K.3 Chain B: D.233, D.234, V.235, D.236 Ligand excluded by PLIP EDO.13: 2 residues within 4Å: Chain B: E.38, R.45 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain B: I.15, E.18, L.19, K.22, E.335 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain B: H.315, G.316, F.317, F.390 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain B: R.62, K.286, E.289, I.290, N.293 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain B: I.15, Y.27, F.338, V.355 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain B: K.22, L.24, W.339, M.343 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ikushiro, H. et al., Structural insights into the substrate recognition of serine palmitoyltransferase from Sphingobacterium multivorum. J.Biol.Chem. (2023)

Release Date

2023-08-16

Peptides

Serine palmitoyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Serine palmitoyltransferase

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