SMTL ID : 8iyp.1

Crystal structure of serine palmitoyltransferase soaked in 190 mM D-serine solution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

2 x PLS: [3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE(Non-covalent)

PLS.1: 18 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, T.241, S.243, K.244 Chain B: S.81, M.271, F.272, S.273, A.274 23 PLIP interactions: 4 interactions with chain B, 19 interactions with chain A Hydrogen bonds: B:S.81, B:A.274, A:N.52, A:G.113, A:F.114, A:N.117, A:S.140, A:S.243, A:S.243, A:K.244 Water bridges: B:S.81, B:S.81, A:D.181, 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 PLS.9: 18 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, T.241, S.243, K.244 22 PLIP interactions: 18 interactions with chain B, 4 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:S.140, B:T.241, B:S.243, B:S.243, B:K.244, A:S.81, A:A.274 Water bridges: B:D.181, B:S.185, B:S.185, B:H.213, A:S.81, A:S.81 Salt bridges: B:H.138, B:K.244 pi-Stacking: B:H.138

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

EDO.2: 6 residues within 4Å: Chain A: S.2, K.3 Chain B: D.233, D.234, V.235, D.236 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:S.2, A:S.2 Water bridges: A:G.4, B:K.104, B:D.256, B:D.256, B:D.256 EDO.3: 2 residues within 4Å: Chain A: E.38, R.45 No protein-ligand interaction detected (PLIP) EDO.4: 5 residues within 4Å: Chain A: R.62, K.286, E.289, I.290, N.293 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.286, A:K.286, A:N.293 EDO.5: 4 residues within 4Å: Chain A: H.315, G.316, F.317, F.390 No protein-ligand interaction detected (PLIP) EDO.6: 5 residues within 4Å: Chain A: I.10, S.11, F.13, K.14 Chain B: D.258 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.258, B:D.258, A:S.11, A:K.14 EDO.7: 3 residues within 4Å: Chain A: Y.101, H.220, A.223 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.292 EDO.8: 5 residues within 4Å: Chain A: I.15, Y.27, V.355 Chain B: F.83, H.265 No protein-ligand interaction detected (PLIP) EDO.10: 6 residues within 4Å: Chain A: D.233, D.234, V.235, D.236 Chain B: S.2, K.3 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:S.2 Water bridges: B:S.2, B:G.4, A:K.104, A:D.256, A:D.256, A:D.256 EDO.11: 2 residues within 4Å: Chain B: E.38, R.45 No protein-ligand interaction detected (PLIP) EDO.12: 5 residues within 4Å: Chain B: R.62, K.286, E.289, I.290, N.293 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.286, B:K.286, B:E.289, B:N.293 EDO.13: 4 residues within 4Å: Chain B: H.315, G.316, F.317, F.390 No protein-ligand interaction detected (PLIP) EDO.14: 5 residues within 4Å: Chain A: D.258 Chain B: I.10, S.11, F.13, K.14 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.11, B:K.14, A:D.258 EDO.15: 3 residues within 4Å: Chain B: Y.101, H.220, A.223 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Q.292 EDO.16: 5 residues within 4Å: Chain A: F.83, H.265 Chain B: I.15, Y.27, V.355 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.27

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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