SMTL ID : 8i09.2 (2 other biounits)

Crystal structure of serine acetyltransferase from Salmonella typhimurium complexed with butyl gallate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-hexamer

Ligands

6 x CYS: CYSTEINE(Non-covalent)

CYS.1: 7 residues within 4Å: Chain A: D.100, P.101, A.102, D.165, H.166 Chain B: R.200, H.201 6 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A, 1 Ligand-Ligand interactions Salt bridges: B:R.200, B:H.201 Hydrogen bonds: A:D.100, A:D.100, A:A.102, C.1 CYS.3: 7 residues within 4Å: Chain B: D.100, P.101, A.102, D.165, H.166 Chain C: R.200, H.201 5 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions, 2 interactions with chain C Hydrogen bonds: B:D.100, B:D.100, C.3 Salt bridges: C:R.200, C:H.201 CYS.6: 6 residues within 4Å: Chain A: R.200, H.201 Chain C: D.100, P.101, D.165, H.166 5 PLIP interactions: 1 Ligand-Ligand interactions, 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: C.6, C:D.100, C:D.165 Salt bridges: A:R.200, A:H.201 CYS.8: 7 residues within 4Å: Chain D: D.100, P.101, A.102, D.165, H.166 Chain E: R.200, H.201 6 PLIP interactions: 3 interactions with chain D, 2 interactions with chain E, 1 Ligand-Ligand interactions Hydrogen bonds: D:D.100, D:D.100, D:A.102, C.8 Salt bridges: E:R.200, E:H.201 CYS.10: 7 residues within 4Å: Chain E: D.100, P.101, A.102, D.165, H.166 Chain F: R.200, H.201 5 PLIP interactions: 2 interactions with chain F, 2 interactions with chain E, 1 Ligand-Ligand interactions Salt bridges: F:R.200, F:H.201 Hydrogen bonds: E:D.100, E:D.100, C.10 CYS.13: 6 residues within 4Å: Chain D: R.200, H.201 Chain F: D.100, P.101, D.165, H.166 5 PLIP interactions: 2 interactions with chain D, 2 interactions with chain F, 1 Ligand-Ligand interactions Salt bridges: D:R.200, D:H.201 Hydrogen bonds: F:D.100, F:D.165, C.13

6 x NF0: butyl 3,4,5-tris(oxidanyl)benzoate(Non-covalent)

NF0.2: 14 residues within 4Å: Chain B: L.185, M.209, I.210, G.211, K.227, I.228, G.229, A.230, A.245 Chain C: G.192, T.193, G.194, L.217, L.235 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:K.227, B:A.245, C:L.217, C:L.235 Hydrogen bonds: B:I.228 Salt bridges: B:K.227 pi-Cation interactions: B:K.227 NF0.4: 12 residues within 4Å: Chain A: M.209, I.210, G.211, K.227, I.228, G.229, A.230, A.245 Chain B: G.192, T.193, G.194, L.235 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.245, B:L.235 Hydrogen bonds: A:I.228 Salt bridges: A:K.227 NF0.5: 14 residues within 4Å: Chain A: G.192, T.193, G.194, L.217, L.235 Chain C: L.185, M.209, I.210, G.211, K.227, I.228, G.229, A.230, A.245 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:M.209 Salt bridges: C:K.227 pi-Cation interactions: C:K.227 Hydrophobic interactions: A:L.217, A:L.235 Water bridges: A:K.195 NF0.9: 14 residues within 4Å: Chain E: L.185, M.209, I.210, G.211, K.227, I.228, G.229, A.230, A.245 Chain F: G.192, T.193, G.194, L.217, L.235 7 PLIP interactions: 5 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: E:K.227, E:A.245, F:L.217, F:L.235 Hydrogen bonds: E:I.228 Salt bridges: E:K.227 pi-Cation interactions: E:K.227 NF0.11: 12 residues within 4Å: Chain D: M.209, I.210, G.211, K.227, I.228, G.229, A.230, A.245 Chain E: G.192, T.193, G.194, L.235 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain D Hydrophobic interactions: E:L.235, D:A.245 Hydrogen bonds: D:I.228 Salt bridges: D:K.227 NF0.12: 14 residues within 4Å: Chain D: G.192, T.193, G.194, L.217, L.235 Chain F: L.185, M.209, I.210, G.211, K.227, I.228, G.229, A.230, A.245 6 PLIP interactions: 3 interactions with chain F, 3 interactions with chain D Hydrogen bonds: F:M.209 Salt bridges: F:K.227 pi-Cation interactions: F:K.227 Hydrophobic interactions: D:L.217, D:L.235 Water bridges: D:K.195

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.7: 8 residues within 4Å: Chain A: S.187, G.213, K.215 Chain B: S.187, K.215 Chain C: S.187, G.213, K.215 7 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A, 2 interactions with chain C Hydrogen bonds: B:S.187, A:S.187, A:S.187, C:S.187 Salt bridges: B:K.215, A:K.215, C:K.215 PO4.14: 8 residues within 4Å: Chain D: S.187, G.213, K.215 Chain E: S.187, K.215 Chain F: S.187, G.213, K.215 7 PLIP interactions: 2 interactions with chain E, 2 interactions with chain F, 3 interactions with chain D Hydrogen bonds: E:S.187, F:S.187, D:S.187, D:S.187 Salt bridges: E:K.215, F:K.215, D:K.215

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Toyomoto, T. et al., Alkyl gallates inhibit serine O -acetyltransferase in bacteria and enhance susceptibility of drug-resistant Gram-negative bacteria to antibiotics. Front Microbiol (2023)

Release Date

2023-11-22

Peptides

Serine acetyltransferase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

D
D

E
E

F
F

Serine acetyltransferase

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