SMTL ID : 3dwp.1

Crystal structure of the B-subunit of the AB5 toxin from E. Coli with Neu5Gc

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-pentamer

Ligands

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

NGC.1: 8 residues within 4Å: Chain A: G.9, M.10, F.11, S.12, Q.36, S.40, Y.78, K.115 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:M.10, A:M.10, A:S.12, A:Q.36, A:Q.36, A:S.40, A:S.40, A:Y.78, A:Y.78 Water bridges: A:S.12, A:S.12 NGC.3: 9 residues within 4Å: Chain B: D.8, G.9, M.10, F.11, S.12, Q.36, Y.78, T.107, K.115 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:M.10, B:M.10, B:S.12, B:Q.36, B:Q.36, B:Y.78, B:Y.78, B:T.107 Water bridges: B:S.12, B:T.107 NGC.5: 8 residues within 4Å: Chain C: D.8, G.9, M.10, F.11, S.12, Q.36, Y.78, K.115 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:M.10, C:M.10, C:S.12, C:Q.36, C:Q.36, C:Y.78, C:Y.78 Water bridges: C:S.12, C:S.12, C:S.40, C:S.40 NGC.7: 8 residues within 4Å: Chain D: D.8, G.9, M.10, F.11, S.12, Q.36, Y.78, K.115 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:M.10, D:M.10, D:S.12, D:Q.36, D:Q.36, D:S.40, D:S.40, D:Y.78, D:Y.78 Water bridges: D:R.75, D:T.107 NGC.9: 9 residues within 4Å: Chain E: D.8, G.9, M.10, F.11, S.12, Q.36, S.40, Y.78, K.115 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:M.10, E:M.10, E:S.12, E:Q.36, E:Q.36, E:S.40, E:S.40, E:Y.78, E:Y.78 Water bridges: E:S.12, E:S.12

5 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.2: 9 residues within 4Å: Chain A: N.62, L.65, Y.66, T.69, T.70 Chain C: L.65 Chain E: Y.66 Ligands: 1PE.6, 1PE.10 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:T.69 Water bridges: C:N.62 1PE.4: 10 residues within 4Å: Chain B: N.62, L.65, Y.66, T.69, T.70 Chain D: Y.66 Chain E: L.65, T.69 Ligands: 1PE.8, 1PE.10 2 PLIP interactions: 2 interactions with chain B Water bridges: B:Y.66, B:Y.66 1PE.6: 9 residues within 4Å: Chain C: N.62, L.65, Y.66, T.69, T.70 Chain D: L.65, T.69 Ligands: 1PE.2, 1PE.8 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Water bridges: D:T.69 Hydrogen bonds: C:T.69 1PE.8: 7 residues within 4Å: Chain B: T.69 Chain D: N.62, Y.66, T.69, T.70 Ligands: 1PE.4, 1PE.6 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Water bridges: D:N.62, D:N.62, B:Y.68 1PE.10: 6 residues within 4Å: Chain E: N.62, Y.66, T.69, T.70 Ligands: 1PE.2, 1PE.4 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Byres, E. et al., Incorporation of a non-human glycan mediates human susceptibility to a bacterial toxin. Nature (2008)

Release Date

2008-11-04

Peptides

Subtilase cytotoxin, subunit B: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Subtilase cytotoxin, subunit B

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