SMTL ID : 7ee5.1

Crystal structure of Neu5Gc bound PltC

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.24 Å

Oligo State

homo-pentamer

Ligands

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

GLC-GAL-NGC.1: 8 residues within 4Å: Chain A: T.7, Y.8, V.9, S.10, N.11, H.38, I.43, Y.82 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.11, A:Y.8, A:Y.8, A:Y.8, A:S.10, A:Y.82 Water bridges: A:S.10, A:S.10, A:S.10, A:S.10, A:H.38, A:S.10, A:S.10, A:Y.82 GLC-GAL-NGC.2: 10 residues within 4Å: Chain E: S.24, G.25, V.51, Y.54, G.55, V.86, W.87, R.88, D.89, F.92 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:R.88, E:S.24, E:Y.54, E:V.86, E:R.88, E:D.89, E:D.89 Water bridges: E:R.88, E:R.88, E:G.25, E:G.55, E:G.55 Salt bridges: E:R.88

2 x NGC: N-glycolyl-alpha-neuraminic acid(Non-covalent)

NGC.3: 11 residues within 4Å: Chain A: S.24, G.25, K.27, V.51, Y.54, G.55, V.86, W.87, R.88, D.89, F.92 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.24, A:Y.54, A:G.55, A:V.86, A:R.88, A:D.89 Water bridges: A:G.25, A:K.27, A:K.27 Salt bridges: A:K.27 NGC.6: 9 residues within 4Å: Chain D: S.24, G.25, V.51, Y.54, G.55, V.86, W.87, R.88, D.89 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:S.24, D:Y.54, D:G.55, D:V.86, D:R.88, D:D.89 Water bridges: D:S.24, D:G.25

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.4: 12 residues within 4Å: Chain B: Y.22, S.24, T.29, V.51, Y.54, G.55, V.86, W.87, R.88, D.89, F.92 Ligands: PG4.5 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.24, B:T.29, B:T.29, B:R.88, B:D.89 PG4.5: 6 residues within 4Å: Chain B: V.53, Y.54, G.55, N.56, K.58 Ligands: PG4.4 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.55, B:N.56, B:K.58

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, X. et al., Molecular Insights into the Assembly and Functional Diversification of Typhoid Toxin. Mbio (2022)

Release Date

2021-12-22

Peptides

Subtilase cytotoxin subunit B-like protein: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Subtilase cytotoxin subunit B-like protein

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