SMTL ID : 6hmy.1 (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: 14 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, K.34, R.35 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.14, A:Q.56, A:Q.61, A:Q.61, A:K.91, A:E.11, A:H.13 Water bridges: A:K.91, A:H.13, A:H.13, A:I.58, A:Q.61, A:Q.61, B:K.34 Hydrophobic interactions: A:H.13, B:R.35 BGC-GAL-NGA-GAL-FUC-SIA.2: 14 residues within 4Å: Chain B: E.11, Y.12, H.13, N.14, E.51, Q.56, H.57, I.58, Q.61, W.88, K.91 Chain C: G.33, K.34, R.35 5 PLIP interactions: 5 interactions with chain B Water bridges: B:K.91, B:K.91, B:H.13, B:H.13, B:I.58, B:Q.61 Hydrogen bonds: B:Q.61, B:Q.61, B:K.91, B:E.11, B:H.13 Hydrophobic interactions: B:H.13 Salt bridges: B: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 7 PLIP interactions: 7 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:H.13, D:I.58, D:Q.61 Hydrophobic interactions: D:H.13, D:E.11, D:Y.12 Salt bridges: D:H.13 BGC-GAL-NGA-GAL-FUC-SIA.5: 14 residues within 4Å: Chain A: G.33, K.34 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 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:Q.56, E:H.13 Hydrogen bonds: E:N.90, E:Q.61, E:Q.61, E:N.90, E:N.90, E:K.91, E:E.11, E:H.13 Water bridges: E:K.91, E:K.91, E:H.13, E:H.13, E:I.58, E:Q.61, E:Q.61 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.3: 14 residues within 4Å: Chain C: E.11, Y.12, H.13, N.14, E.51, Q.56, I.58, Q.61, W.88, N.90, K.91 Chain D: G.33, K.34, R.35 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Water bridges: C:N.90, C:K.91, C:K.91, C:H.13, C:H.13, D:G.33, C:I.58, C:Q.61 Hydrogen bonds: C:Q.61, C:Q.61, C:N.90, C:N.90, C:K.91, C:E.11, C:H.13 Hydrophobic interactions: C:H.13 Salt bridges: C:H.13

10 x CA: CALCIUM ION(Non-covalent)

CA.6: 2 residues within 4Å: Chain A: E.79 Ligands: BCN.8 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.79, A:E.79 CA.9: 2 residues within 4Å: Chain A: E.79 Ligands: BCN.7 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.79, H2O.15 CA.11: 2 residues within 4Å: Chain B: E.79 Ligands: BCN.13 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.79, B:E.79 CA.12: 2 residues within 4Å: Chain B: E.79 Ligands: BCN.10 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.79, H2O.2 CA.15: 2 residues within 4Å: Chain C: E.79 Ligands: BCN.16 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.79, C:E.79 CA.17: 2 residues within 4Å: Chain C: E.79 Ligands: BCN.14 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.79, H2O.5 CA.19: 2 residues within 4Å: Chain D: E.79 Ligands: BCN.21 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.79, D:E.79 CA.20: 2 residues within 4Å: Chain D: E.79 Ligands: BCN.18 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.79, H2O.7 CA.23: 2 residues within 4Å: Chain E: E.79 Ligands: BCN.24 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:E.79, E:E.79 CA.25: 2 residues within 4Å: Chain E: E.79 Ligands: BCN.22 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.79, H2O.14

10 x BCN: BICINE(Non-covalent)

BCN.7: 7 residues within 4Å: Chain A: Y.76, L.77, E.79 Chain E: A.80, K.81, N.103 Ligands: CA.9 6 PLIP interactions: 3 interactions with chain E, 3 interactions with chain A Hydrogen bonds: E:K.81, E:N.103 Water bridges: E:N.103, A:E.79, A:E.79 Salt bridges: A:E.79 BCN.8: 2 residues within 4Å: Chain A: E.79 Ligands: CA.6 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.23 Salt bridges: A:K.23, A:E.79 BCN.10: 8 residues within 4Å: Chain A: A.80, K.81, N.103 Chain B: Y.76, L.77, E.79 Ligands: CA.12, BCN.13 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Water bridges: B:E.79, A:K.81, A:A.102 Salt bridges: B:E.79 Hydrogen bonds: A:K.81, A:N.103 BCN.13: 3 residues within 4Å: Chain B: E.79 Ligands: BCN.10, CA.11 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.23, B:E.79 BCN.14: 8 residues within 4Å: Chain B: A.80, K.81, N.103 Chain C: Y.76, L.77, E.79 Ligands: BCN.16, CA.17 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:K.81, B:N.103, C:E.79 Salt bridges: B:K.81, C:E.79 Water bridges: C:E.79 BCN.16: 3 residues within 4Å: Chain C: E.79 Ligands: BCN.14, CA.15 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:E.79 BCN.18: 7 residues within 4Å: Chain C: A.80, K.81, N.103 Chain D: Y.76, L.77, E.79 Ligands: CA.20 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:K.81, C:N.103, C:N.103, C:N.103 Water bridges: C:K.81, C:A.102, D:E.79 Salt bridges: D:E.79 BCN.21: 3 residues within 4Å: Chain D: K.23, E.79 Ligands: CA.19 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:E.79 Water bridges: D:K.23, D:K.23, D:K.23, D:K.23 Salt bridges: D:K.23, D:E.79 BCN.22: 8 residues within 4Å: Chain D: A.80, K.81, N.103 Chain E: Y.76, L.77, E.79 Ligands: BCN.24, CA.25 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:K.81 Water bridges: D:K.81, D:A.102, D:N.103, D:N.103, E:E.79 Salt bridges: E:E.79 BCN.24: 3 residues within 4Å: Chain E: E.79 Ligands: BCN.22, CA.23 3 PLIP interactions: 3 interactions with chain E Water bridges: E:E.79, E:E.79 Salt bridges: E:E.79

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
A

B
B

C
C

D
D

E
E

Cholera enterotoxin B-subunit

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