SMTL ID : 6hmw.1 (1 other biounit)

Cholera toxin classical B-pentamer in complex with fucose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-pentamer

Ligands

10 x CA: CALCIUM ION(Non-covalent)

CA.1: 2 residues within 4Å: Chain A: E.79 Ligands: BCN.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.79, A:E.79 CA.4: 2 residues within 4Å: Chain A: E.79 Ligands: BCN.2 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.79, H2O.5 CA.8: 3 residues within 4Å: Chain B: E.79 Ligands: BCN.10, CA.11 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.79, B:E.79, H2O.2 CA.11: 3 residues within 4Å: Chain B: E.79 Ligands: BCN.6, CA.8 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.79, H2O.3 CA.13: 2 residues within 4Å: Chain C: E.79 Ligands: BCN.17 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.79, C:E.79, H2O.4 CA.15: 2 residues within 4Å: Chain C: E.79 Ligands: BCN.16 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.79, H2O.2 CA.20: 2 residues within 4Å: Chain D: E.79 Ligands: BCN.22 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.79, D:E.79 CA.23: 2 residues within 4Å: Chain D: E.79 Ligands: BCN.18 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.79 CA.26: 4 residues within 4Å: Chain E: K.23, E.79 Ligands: CA.28, BCN.29 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:E.79, E:E.79 CA.28: 3 residues within 4Å: Chain E: E.79 Ligands: BCN.24, CA.26 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.79, H2O.4

10 x BCN: BICINE(Non-covalent)

BCN.2: 8 residues within 4Å: Chain A: Y.76, L.77, E.79 Chain E: A.80, K.81, N.103 Ligands: CA.4, BCN.5 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:K.81, E:N.103 Water bridges: A:E.79 Salt bridges: A:E.79 BCN.5: 4 residues within 4Å: Chain A: K.23, E.79 Ligands: CA.1, BCN.2 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.23, A:E.79 BCN.6: 8 residues within 4Å: Chain A: A.80, K.81, N.103 Chain B: Y.76, L.77, E.79 Ligands: BCN.10, CA.11 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Salt bridges: B:E.79 Hydrogen bonds: A:K.81, A:N.103 Water bridges: A:N.103, A:N.103 BCN.10: 3 residues within 4Å: Chain B: E.79 Ligands: BCN.6, CA.8 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.23 Salt bridges: B:E.79 BCN.16: 7 residues within 4Å: Chain B: A.80, K.81, N.103 Chain C: Y.76, L.77, E.79 Ligands: CA.15 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:K.81, B:N.103, C:E.79 Water bridges: B:K.81, B:A.102 Salt bridges: C:E.79 BCN.17: 3 residues within 4Å: Chain C: K.23, E.79 Ligands: CA.13 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.79, C:E.79 Salt bridges: C:K.23, C:E.79 BCN.18: 8 residues within 4Å: Chain C: A.80, K.81, N.103 Chain D: Y.76, L.77, E.79 Ligands: BCN.22, CA.23 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:K.81, C:N.103 Water bridges: C:K.81, C:A.102, D:E.79 Salt bridges: D:E.79 BCN.22: 4 residues within 4Å: Chain D: K.23, E.79 Ligands: BCN.18, CA.20 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:K.23, D:E.79 BCN.24: 8 residues within 4Å: Chain D: A.80, K.81, N.103 Chain E: Y.76, L.77, E.79 Ligands: CA.28, BCN.29 7 PLIP interactions: 3 interactions with chain E, 4 interactions with chain D Hydrogen bonds: E:E.79, D:K.81, D:N.103 Water bridges: E:E.79, D:K.81, D:N.103 Salt bridges: E:E.79 BCN.29: 4 residues within 4Å: Chain E: K.23, E.79 Ligands: BCN.24, CA.26 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:E.79 Salt bridges: E:K.23, E:E.79

9 x FUL: beta-L-fucopyranose(Non-covalent)(Post Translational Modification)

FUL.3: 9 residues within 4Å: Chain A: H.18, G.45, A.46, T.47, F.48, T.92, P.93, H.94 Chain E: Q.3 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain E Hydrophobic interactions: A:F.48 Hydrogen bonds: A:T.47, A:H.94, E:Q.3, E:Q.3, E:Q.3 FUL.7: 4 residues within 4Å: Chain B: T.1, P.2, E.11 Chain C: R.35 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:E.11 Hydrogen bonds: B:T.1 FUL.9: 9 residues within 4Å: Chain A: Q.3 Chain B: H.18, G.45, A.46, T.47, F.48, T.92, P.93, H.94 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.48 Hydrogen bonds: B:T.47, B:H.94, B:H.94, A:Q.3, A:Q.3, A:Q.3 FUL.12: 4 residues within 4Å: Chain C: T.1, P.2, E.11 Chain D: R.35 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:R.35, C:T.1 Hydrophobic interactions: C:P.2 FUL.14: 3 residues within 4Å: Chain C: T.6, I.17, K.84 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.6, C:K.84, C:K.84 FUL.19: 4 residues within 4Å: Chain D: T.1, P.2, E.11 Chain E: R.35 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:R.35, D:T.1 Hydrophobic interactions: D:E.11 FUL.21: 9 residues within 4Å: Chain C: Q.3 Chain D: H.18, G.45, A.46, T.47, F.48, T.92, P.93, H.94 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:F.48 Hydrogen bonds: D:T.47, D:T.47, D:H.94, C:Q.3, C:Q.3, C:Q.3 FUL.25: 3 residues within 4Å: Chain E: T.1, P.2, E.11 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:E.11 Hydrogen bonds: E:T.1 FUL.27: 9 residues within 4Å: Chain D: Q.3 Chain E: H.18, G.45, A.46, T.47, F.48, T.92, P.93, H.94 7 PLIP interactions: 4 interactions with chain E, 3 interactions with chain D Hydrophobic interactions: E:F.48 Hydrogen bonds: E:T.47, E:T.47, E:H.94, D:Q.3, D:Q.3, D: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 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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