SMTL ID : 5wht.1

Crystal structure of 3'SL bound PltB

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-pentamer

Ligands

1 x GLC- GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose

GLC-GAL-SIA.1: 6 residues within 4Å: Chain A: A.32, Y.33, Y.34, S.35, D.36, K.59 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.35, A:Y.33, A:Y.33, A:S.35, A:K.59 Water bridges: A:S.35, A:D.36, A:D.36, A:D.36, A:R.100, A:R.100, A:Y.33, A:R.100 Hydrophobic interactions: A:A.32, A:Y.33, A:Y.34 Salt bridges: A:K.59

1 x GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose(Non-covalent)

GAL-SIA.2: 6 residues within 4Å: Chain C: A.32, Y.33, Y.34, S.35, D.36, K.59 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:S.35, C:Y.33, C:Y.33, C:S.35, C:K.59 Water bridges: C:D.36, C:D.36, C:R.100, C:Y.33 Hydrophobic interactions: C:A.32, C:Y.33, C:Y.34 Salt bridges: C:K.59

8 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 7 residues within 4Å: Chain A: I.47, D.48, Q.75, W.108, T.109, Y.110, F.113 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.47, A:Y.110 Hydrogen bonds: A:T.109, A:Y.110 ACT.5: 3 residues within 4Å: Chain B: G.62, S.63, G.64 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.63 ACT.6: 6 residues within 4Å: Chain B: I.47, Y.110, P.111, L.112, F.113 Chain E: W.25 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.110, B:L.112 ACT.7: 6 residues within 4Å: Chain A: I.47, D.48, Y.110 Chain B: E.24, W.25, D.28 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.25 Hydrogen bonds: A:Y.110 ACT.9: 5 residues within 4Å: Chain C: Q.75, W.108, T.109, Y.110, F.113 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.108, C:Y.110 ACT.11: 6 residues within 4Å: Chain C: W.25 Chain D: I.47, Y.110, P.111, L.112, F.113 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:Y.110, D:L.112 ACT.12: 6 residues within 4Å: Chain D: E.24, W.25, D.28 Chain E: I.47, D.48, Y.110 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.24, D:E.24 ACT.14: 6 residues within 4Å: Chain E: I.47, Q.75, W.108, T.109, Y.110, F.113 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:W.108, E:Y.110, E:F.113 Hydrogen bonds: E:Q.75, E:T.109

2 x SIA: N-acetyl-alpha-neuraminic acid(Non-covalent)

SIA.4: 5 residues within 4Å: Chain B: A.32, Y.33, Y.34, S.35, K.59 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:A.32, B:Y.33 Hydrogen bonds: B:Y.33, B:Y.33, B:S.35, B:K.59 Water bridges: B:Y.33, B:S.35, B:S.35 Salt bridges: B:K.59 SIA.10: 6 residues within 4Å: Chain D: A.32, Y.33, Y.34, S.35, E.37, K.59 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:A.32, D:Y.33, D:Y.34 Hydrogen bonds: D:Y.33, D:S.35, D:K.59, D:K.59, D:K.59 Water bridges: D:Y.33, D:Y.33 Salt bridges: D:K.59

5 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 6 residues within 4Å: Chain B: V.38, S.40, V.58, K.59, A.60, G.62 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.60 PEG.13: 3 residues within 4Å: Chain D: S.76, I.77 Chain E: T.49 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.76 Water bridges: D:E.24, D:S.76 PEG.15: 4 residues within 4Å: Chain E: Y.33, Y.34, S.35, K.59 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:S.35, E:S.35, E:K.59 Water bridges: E:S.35, E:R.100 PEG.16: 5 residues within 4Å: Chain E: N.106, V.114, S.118, A.119, N.120 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.106 Water bridges: E:F.117 PEG.17: 3 residues within 4Å: Chain D: Q.97 Chain E: Y.93, S.94 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:Y.93, D:Q.97 Water bridges: E:S.40, E:Y.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gao, X. et al., Evolution of host adaptation in the Salmonella typhoid toxin. Nat Microbiol (2017)

Release Date

2017-10-25

Peptides

Putative pertussis-like toxin subunit: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Putative pertussis-like toxin subunit