SMTL ID : 8i09.3 (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: 6 residues within 4Å: Chain A: D.100, P.101, D.165, H.166 Chain B: R.200, H.201 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:H.166 Hydrogen bonds: B:R.200, B:R.200 CYS.5: 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: 3 interactions with chain C, 2 interactions with chain B Water bridges: C:R.200 Salt bridges: C:R.200, C:H.201 Hydrogen bonds: B:D.100, B:A.102 CYS.7: 6 residues within 4Å: Chain A: R.200, H.201 Chain C: D.100, P.101, D.165, H.166 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Water bridges: A:R.200 Salt bridges: A:R.200, A:H.201 Hydrogen bonds: C:D.100 CYS.8: 9 residues within 4Å: Chain D: D.100, H.166 Chain E: V.171, G.173, L.190, G.191, G.192, R.200, H.201 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:D.100, D:H.166 Water bridges: E:R.200 Salt bridges: E:R.200, E:H.201 CYS.9: 6 residues within 4Å: Chain D: G.173, R.200, H.201 Chain F: D.100, D.165, H.166 5 PLIP interactions: 1 Ligand-Ligand interactions, 2 interactions with chain F, 2 interactions with chain D Hydrogen bonds: C.9, F:D.100, F:D.100 Salt bridges: D:R.200, D:H.201 CYS.11: 6 residues within 4Å: Chain E: D.100, P.101, D.165, H.166 Chain F: R.200, H.201 6 PLIP interactions: 3 interactions with chain F, 2 interactions with chain E, 1 Ligand-Ligand interactions Water bridges: F:R.200 Salt bridges: F:R.200, F:H.201 Hydrogen bonds: E:D.100, E:D.100, C.11

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

NF0.2: 15 residues within 4Å: Chain A: L.185, 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.217, V.233, L.235 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:A.245, B:L.217, B:L.235 Hydrogen bonds: A:I.228 Water bridges: A:A.212 Salt bridges: A:K.227 pi-Cation interactions: A:K.227 NF0.4: 15 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, V.233, L.235 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:K.227, B:A.245, C:L.217, C:V.233, C:L.235 Hydrogen bonds: B:I.228 Water bridges: B:A.212 Salt bridges: B:K.227 pi-Cation interactions: B:K.227 NF0.6: 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 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:A.245, A:L.217, A:L.235 Hydrogen bonds: C:I.228, A:G.194 Salt bridges: C:K.227 pi-Cation interactions: C:K.227 NF0.10: 13 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.217, L.235 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:K.227, D:A.245, E:L.217, E:L.235 Hydrogen bonds: D:I.228 Water bridges: D:A.212 Salt bridges: D:K.227 pi-Cation interactions: D:K.227 NF0.13: 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 NF0.14: 13 residues within 4Å: Chain D: G.192, T.193, G.194, L.217, L.235 Chain F: M.209, I.210, G.211, K.227, I.228, G.229, A.230, A.245 8 PLIP interactions: 5 interactions with chain F, 3 interactions with chain D Hydrophobic interactions: F:A.245, D:L.217, D:L.235 Hydrogen bonds: F:I.228 Water bridges: F:A.212, D:G.192 Salt bridges: F:K.227 pi-Cation interactions: F:K.227

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

PO4.3: 9 residues within 4Å: Chain A: S.187, G.213, K.215 Chain B: S.187, G.213, K.215 Chain C: S.187, G.213, K.215 8 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: C:S.187, C:S.187, B:S.187, B:S.187, A:S.187 Salt bridges: C:K.215, B:K.215, A:K.215 PO4.12: 9 residues within 4Å: Chain D: S.187, G.213, K.215 Chain E: S.187, G.213, 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
G

B
H

C
I

D
J

E
K

F
L

Serine acetyltransferase

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