SMTL ID : 6hmy.2 (1 other biounit)

Cholera toxin classical B-pentamer in complex with fucosyl-GM1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-pentamer

Ligands

4 x BGC- GAL- NGA- GAL- FUC- SIA: alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranose

BGC-GAL-NGA-GAL-FUC-SIA.1: 13 residues within 4Å: Chain A: E.11, Y.12, H.13, N.14, E.51, Q.56, H.57, I.58, Q.61, W.88, K.91 Chain B: G.33, R.35 6 PLIP interactions: 6 interactions with chain A Water bridges: A:N.14, A:N.90, A:K.91, A:H.13, A:H.13, A:W.88, A:I.58, A:Q.61 Hydrogen bonds: A:Q.61, A:Q.61, A:K.91, A:E.11, A:H.13, A:H.13 Hydrophobic interactions: A:H.13 Salt bridges: A:H.13 BGC-GAL-NGA-GAL-FUC-SIA.3: 15 residues within 4Å: Chain C: E.11, Y.12, H.13, N.14, E.51, Q.56, H.57, I.58, Q.61, W.88, N.90, K.91 Chain D: G.33, K.34, R.35 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.90, C:N.90, C:Q.61, C:Q.61, C:N.90, C:N.90, C:K.91, C:E.11, C:H.13 Water bridges: C:K.91, C:E.51, C:H.13, C:H.13, C:H.13, C:I.58, C:Q.61, C:Q.61 Hydrophobic interactions: C:H.13 BGC-GAL-NGA-GAL-FUC-SIA.4: 15 residues within 4Å: Chain D: E.11, Y.12, H.13, N.14, E.51, Q.56, H.57, I.58, Q.61, W.88, N.90, K.91 Chain E: G.33, K.34, R.35 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.90, D:Q.61, D:Q.61, D:N.90, D:N.90, D:K.91, D:E.11, D:H.13 Water bridges: D:K.91, D:E.51, D:K.91, D:H.13, D:H.13, D:I.58, D:I.58, D:Q.61 Hydrophobic interactions: D:H.13 BGC-GAL-NGA-GAL-FUC-SIA.5: 14 residues within 4Å: Chain A: G.33, R.35 Chain E: E.11, Y.12, H.13, N.14, E.51, Q.56, H.57, I.58, Q.61, W.88, N.90, K.91 5 PLIP interactions: 5 interactions with chain E Water bridges: E:H.13, E:N.14, E:N.14, E:K.91, E:K.91, E:H.13, E:Q.61 Hydrogen bonds: E:Q.56, E:Q.61, E:Q.61, E:N.90, E:N.90, E:K.91, E:E.11, E:H.13 Hydrophobic interactions: E:E.11 Salt bridges: E:H.13

1 x GLC- GAL- NGA- GAL- FUC- SIA: alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose

GLC-GAL-NGA-GAL-FUC-SIA.2: 14 residues within 4Å: Chain B: E.11, Y.12, H.13, E.51, Q.56, H.57, I.58, Q.61, W.88, N.90, K.91 Chain C: G.33, K.34, R.35 5 PLIP interactions: 5 interactions with chain B Water bridges: B:K.91, B:N.90, B:K.91, B:H.13, B:I.58, B:Q.61 Hydrogen bonds: B:Q.61, B:Q.61, B:N.90, B:K.91, B:E.11, B:H.13 Salt bridges: B:H.13

2 x FUC: alpha-L-fucopyranose(Non-covalent)

FUC.6: 7 residues within 4Å: Chain A: A.46, T.47, F.48, T.92, P.93, H.94 Chain E: Q.3 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: A:F.48 Hydrogen bonds: A:T.47, A:H.94, E:Q.3, E:Q.3 Water bridges: A:T.47 FUC.7: 7 residues within 4Å: Chain D: Q.3 Chain E: A.46, T.47, F.48, T.92, P.93, H.94 7 PLIP interactions: 5 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:A.46, E:F.48 Hydrogen bonds: E:T.47, E:H.94, D:Q.3, D:Q.3 Water bridges: E:T.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Heim, J.B. et al., Crystal structures of cholera toxin in complex with fucosylated receptors point to importance of secondary binding site. Sci Rep (2019)

Release Date

2019-08-14

Peptides

Cholera enterotoxin B-subunit: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
G

C
H

D
I

E
J

Cholera enterotoxin B-subunit

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