SMTL ID : 6tyn.1

Salmonella Typhi PltB Homopentamer with Neu-5NAc-9OAc-alpha-2-3-Gal-beta-1-4-GlcNAc Glycans

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

homo-pentamer

Ligands

5 x NAG- GAL- 5N6: 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Non-functional Binders)

NAG-GAL-5N6.1: 9 residues within 4Å: Chain A: A.9, Y.10, Y.11, S.12, D.13, K.36, N.38, G.41, T.42 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.9, A:Y.11 Hydrogen bonds: A:Y.10, A:S.12, A:K.36, A:K.36, A:T.42, A:K.36, A:K.36, A:K.36, A:N.38 Water bridges: A:Y.10, A:N.38, A:S.40 Salt bridges: A:K.36, A:K.36 NAG-GAL-5N6.2: 9 residues within 4Å: Chain C: A.9, Y.10, Y.11, S.12, D.13, K.36, G.41, T.42, V.44 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:A.9, C:V.44 Hydrogen bonds: C:Y.10, C:S.12, C:K.36, C:K.36, C:T.42, C:R.77 Water bridges: C:Y.10, C:Y.10 Salt bridges: C:K.36 NAG-GAL-5N6.3: 9 residues within 4Å: Chain D: I.24, D.25, Q.52, S.53, I.84, W.85, T.86, Y.87, F.90 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:I.24, D:F.90 Hydrogen bonds: D:Q.52, D:Q.52, D:S.53, D:I.84, D:T.86, D:T.86, D:Y.87 Water bridges: D:D.25, D:Q.52 NAG-GAL-5N6.4: 7 residues within 4Å: Chain E: I.24, D.25, Q.52, S.53, I.84, T.86, Y.87 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:I.24 Hydrogen bonds: E:I.84, E:T.86, E:T.86, E:Y.87 NAG-GAL-5N6.5: 9 residues within 4Å: Chain E: A.9, Y.10, Y.11, S.12, K.36, G.41, T.42, V.44, K.82 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:A.9, E:T.42, E:V.44 Hydrogen bonds: E:Y.10, E:Y.10, E:S.12, E:T.42 Water bridges: E:Y.10 Salt bridges: E:K.36, E:R.77

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Nguyen, T. et al., The role of 9-O-acetylated glycan receptor moieties in the typhoid toxin binding and intoxication. Plos Pathog. (2020)

Release Date

2020-02-12

Peptides

Pertussis like toxin subunit B: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Pertussis like toxin subunit B

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