SMTL ID : 6tyo.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

homo-pentamer

Ligands

5 x NAG- GAL- PKM: 4-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-functional Binders)(Non-covalent)

NAG-GAL-PKM.1: 10 residues within 4Å: Chain A: I.24, D.25, V.49, Q.52, S.53, I.84, W.85, T.86, Y.87, F.90 12 PLIP interactions: 12 interactions with chain A Water bridges: A:T.86, A:T.86, A:I.54 Hydrophobic interactions: A:I.24, A:W.85, A:Y.87, A:F.90 Hydrogen bonds: A:Q.52, A:Q.52, A:S.53, A:T.86, A:T.86, A:T.86, A:Y.87 NAG-GAL-PKM.2: 9 residues within 4Å: Chain C: N.8, A.9, Y.10, Y.11, S.12, D.13, K.36, R.77, K.82 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:D.13, C:Y.10, C:Y.10, C:S.12, C:K.36 Water bridges: C:D.13 Hydrophobic interactions: C:A.9, C:Y.10, C:Y.10 Salt bridges: C:K.36, C:R.77 NAG-GAL-PKM.3: 10 residues within 4Å: Chain D: I.24, D.25, V.49, Q.52, S.53, I.84, W.85, T.86, Y.87, F.90 12 PLIP interactions: 12 interactions with chain D Water bridges: D:T.86, D:T.86, D:I.54 Hydrophobic interactions: D:I.24, D:W.85, D:Y.87, D:F.90 Hydrogen bonds: D:D.25, D:Q.52, D:Q.52, D:S.53, D:T.86, D:T.86, D:Y.87 NAG-GAL-PKM.4: 10 residues within 4Å: Chain E: I.24, D.25, V.49, Q.52, S.53, I.84, W.85, T.86, Y.87, F.90 12 PLIP interactions: 12 interactions with chain E Hydrophobic interactions: E:I.24, E:W.85, E:Y.87, E:F.90 Hydrogen bonds: E:Q.52, E:Q.52, E:S.53, E:T.86, E:T.86, E:T.86, E:Y.87 Water bridges: E:I.54 NAG-GAL-PKM.5: 8 residues within 4Å: Chain E: N.8, A.9, Y.10, Y.11, S.12, D.13, K.36, K.82 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:S.12, E:D.13, E:Y.10, E:Y.10, E:S.12, E:K.36 Hydrophobic interactions: E:A.9, E:Y.10, E:Y.10, E:Y.11 Salt bridges: E:K.36

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: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Pertussis-like toxin subunit

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