SMTL ID : 8iyt.1

Crystal Structure of Serine Palmitoyltransferase complexed with D-methylserine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x S5R: (2~{R})-2-methyl-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]-3-oxidanyl-propanoic acid(Non-covalent)

S5R.1: 18 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, T.241, S.243, K.244 Chain B: M.271, F.272, S.273, A.274 23 PLIP interactions: 5 interactions with chain B, 18 interactions with chain A Hydrogen bonds: B:S.81, B:S.273, B:S.273, B:A.274, A:N.52, A:G.113, A:F.114, A:N.117, A:H.138, A:S.140, A:S.243 Water bridges: B:S.81, A:N.52, A:S.185, A:S.185, A:H.213, A:T.241, A:T.241 Hydrophobic interactions: A:H.138, A:A.212 Salt bridges: A:H.138, A:K.244 pi-Stacking: A:H.138 S5R.6: 18 residues within 4Å: Chain A: M.271, 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, T.241, S.243, K.244 22 PLIP interactions: 17 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:H.138, B:A.212 Hydrogen bonds: B:N.52, B:G.113, B:F.114, B:N.117, B:H.138, B:S.140, B:T.241, B:S.243, A:S.81, A:S.273, A:S.273, A:A.274 Water bridges: B:N.52, B:S.185, B:S.185, B:H.213, A:S.81 Salt bridges: B:H.138, B:K.244 pi-Stacking: B:H.138

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

EDO.2: 2 residues within 4Å: Chain A: D.314, H.315 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.314, A:D.314 EDO.3: 6 residues within 4Å: Chain A: R.62, K.286, E.289, I.290, N.293, E.294 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.286, A:E.289, A:E.289, A:N.293, A:E.294 EDO.4: 7 residues within 4Å: Chain A: I.15, E.18, L.19, K.22, L.24, E.335, F.338 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.18, A:K.22 EDO.5: 3 residues within 4Å: Chain A: H.315, G.316, F.317 No protein-ligand interaction detected (PLIP) EDO.7: 2 residues within 4Å: Chain B: D.314, H.315 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.314, B:D.314 EDO.8: 6 residues within 4Å: Chain B: R.62, K.286, E.289, I.290, N.293, E.294 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.286, B:E.289, B:N.293, B:E.294, B:E.294 EDO.9: 7 residues within 4Å: Chain B: I.15, E.18, L.19, K.22, L.24, E.335, F.338 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.18, B:E.18, B:K.22 EDO.10: 3 residues within 4Å: Chain B: H.315, G.316, F.317 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Murakami, T. et al., Crystal structure of Serine Palmitoyltransferase from Sphingobacterium multivorum. To Be Published

Release Date

2024-04-10

Peptides

Serine palmitoyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Serine palmitoyltransferase

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