SMTL ID : 8guh.1

Serine Palmitoyltransferase from Sphingobacterium multivorum complexed with Tris

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

2 x K9E: [4-[[[2-(hydroxymethyl)-1,3-bis(oxidanyl)propan-2-yl]amino]methyl]-6-methyl-5-oxidanyl-pyridin-3-yl]methyl dihydrogen phosphate(Non-covalent)

K9E.1: 19 residues within 4Å: Chain A: N.52, 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, F.272, S.273, A.274 19 PLIP interactions: 15 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:H.138, A:A.212 Hydrogen bonds: A:G.113, A:F.114, A:N.117, A:S.140, A:S.243, A:K.244, B:S.273, B:A.274 Water bridges: A:N.52, A:S.185, A:S.185, A:T.241, A:T.241, B:S.273, B:A.274 Salt bridges: A:K.244 pi-Stacking: A:H.138 K9E.8: 19 residues within 4Å: Chain A: S.81, F.272, S.273, A.274 Chain B: N.52, 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 18 PLIP interactions: 14 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:H.138, B:A.212 Hydrogen bonds: B:G.113, B:F.114, B:N.117, B:S.140, B:T.241, B:S.243, B:K.244, A:S.273, A:A.274 Water bridges: B:N.52, B:S.185, B:S.185, A:S.273, A:A.274 Salt bridges: B:K.244 pi-Stacking: B:H.138

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

EDO.2: 4 residues within 4Å: Chain A: F.13, I.15, Y.27, V.355 2 PLIP interactions: 2 interactions with chain A Water bridges: A:V.355, A:S.356 EDO.3: 6 residues within 4Å: Chain A: I.15, L.19, K.22, L.24, E.335, F.338 No protein-ligand interaction detected (PLIP) EDO.4: 3 residues within 4Å: Chain A: E.38, K.40, R.45 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.45 EDO.5: 2 residues within 4Å: Chain A: E.38, R.45 No protein-ligand interaction detected (PLIP) EDO.6: 5 residues within 4Å: Chain A: R.62, E.289, I.290, N.293, E.294 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.289, A:E.289, A:N.293, A:E.294 EDO.7: 2 residues within 4Å: Chain A: H.315, V.387 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.315 EDO.9: 4 residues within 4Å: Chain B: F.13, I.15, Y.27, V.355 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.27 Water bridges: B:V.355, B:S.356 EDO.10: 6 residues within 4Å: Chain B: I.15, L.19, K.22, L.24, E.335, F.338 No protein-ligand interaction detected (PLIP) EDO.11: 3 residues within 4Å: Chain B: E.38, K.40, R.45 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.45 EDO.12: 2 residues within 4Å: Chain B: E.38, R.45 No protein-ligand interaction detected (PLIP) EDO.13: 5 residues within 4Å: Chain B: R.62, E.289, I.290, N.293, E.294 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.289, B:N.293, B:E.294, B:E.294 EDO.14: 2 residues within 4Å: Chain B: H.315, V.387 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.315

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ikushiro, H. et al., Crystal structure of Sphingobacterium multivorum serine palmitoyltransferase complexed with tris(hydroxymethyl)aminomethane. Acta Crystallogr.,Sect.F (2022)

Release Date

2023-07-19

Peptides

Serine palmitoyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Serine palmitoyltransferase

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