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

Cholera toxin classical B-pentamer in complex with Lewis-x

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

homo-pentamer

Ligands

3 x NDG- FUC- GAL: alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]2-acetamido-2-deoxy-alpha-D-glucopyranose

NDG-FUC-GAL.1: 11 residues within 4Å: Chain A: Q.3 Chain B: Q.16, H.18, N.44, G.45, A.46, T.47, F.48, T.92, P.93, H.94 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.48 Hydrogen bonds: B:T.47, B:T.92, B:H.94, A:Q.3, A:Q.3, B:Q.16, B:H.18, B:H.94, B:G.45, B:G.45 NDG-FUC-GAL.2: 11 residues within 4Å: Chain B: Q.3 Chain C: Q.16, H.18, N.44, G.45, A.46, T.47, F.48, T.92, P.93, H.94 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:F.48 Hydrogen bonds: C:T.47, C:H.94, B:Q.3, B:Q.3, C:Q.16, C:H.94, C:G.45, C:G.45 Water bridges: B:Q.3 NDG-FUC-GAL.3: 11 residues within 4Å: Chain C: Q.3 Chain D: Q.16, H.18, N.44, G.45, A.46, T.47, F.48, T.92, P.93, H.94 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Q.3, C:Q.3, D:T.47, D:H.94, D:Q.16, D:H.94, D:G.45, D:G.45 Hydrophobic interactions: D:F.48

5 x CA: CALCIUM ION(Non-covalent)

CA.4: 2 residues within 4Å: Chain A: E.79 Ligands: BCN.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.79, A:E.79, H2O.2 CA.7: 1 residues within 4Å: Chain B: E.79 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.79, B:E.79 CA.10: 1 residues within 4Å: Chain C: E.79 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.79, C:E.79 CA.11: 1 residues within 4Å: Chain D: E.79 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.79, D:E.79 CA.14: 1 residues within 4Å: Chain E: E.79 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:E.79, E:E.79

6 x BCN: BICINE(Non-covalent)

BCN.5: 3 residues within 4Å: Chain A: K.23, E.79 Ligands: CA.4 4 PLIP interactions: 4 interactions with chain A Water bridges: A:E.79, A:E.79 Salt bridges: A:K.23, A:E.79 BCN.8: 7 residues within 4Å: Chain B: A.80, K.81, N.103 Chain C: K.23, Y.76, L.77, E.79 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:K.23, C:K.23, B:K.81, B:N.103 Salt bridges: C:E.79 Water bridges: B:K.81, B:A.102 BCN.9: 7 residues within 4Å: Chain A: A.80, K.81, N.103 Chain B: K.23, Y.76, L.77, E.79 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.81, A:N.103, A:N.103 Water bridges: A:K.81 Salt bridges: B:E.79 BCN.12: 6 residues within 4Å: Chain D: A.80, K.81, N.103 Chain E: Y.76, L.77, E.79 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:K.81, D:N.103 Water bridges: D:N.103, D:N.103, E:E.79 Salt bridges: E:E.79 BCN.13: 6 residues within 4Å: Chain C: A.80, K.81, N.103 Chain D: Y.76, L.77, E.79 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain C Water bridges: D:E.79, C:K.81, C:A.102 Salt bridges: D:E.79 Hydrogen bonds: C:K.81, C:N.103 BCN.15: 6 residues within 4Å: Chain A: Y.76, L.77, E.79 Chain E: A.80, K.81, N.103 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:K.81, E:N.103 Water bridges: E:N.103, A:E.79 Salt bridges: A:E.79

1 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 5 PLIP interactions: 3 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

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 toxin B subunit: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
G

C
H

D
I

E
J

Cholera toxin B subunit

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