SMTL ID : 5elf.1 (1 other biounit)

Cholera toxin El Tor B-pentamer in complex with A-pentasaccharide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-pentamer

Ligands

2 x GLC- GAL- FUC- A2G- FUC: alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]alpha-D-glucopyranose(Non-covalent)

GLC-GAL-FUC-A2G-FUC.1: 12 residues within 4Å: Chain A: Q.16, I.17, Y.18, N.44, G.45, A.46, I.47, F.48, T.92, P.93, H.94 Chain E: Q.3 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:Q.16, A:Y.18, A:Y.18, A:I.47, A:H.94, E:Q.3, E:Q.3, A:Y.18, A:Y.18, A:G.45 Hydrophobic interactions: A:Y.18, A:F.48 GLC-GAL-FUC-A2G-FUC.3: 12 residues within 4Å: Chain D: Q.3 Chain E: Q.16, I.17, Y.18, N.44, G.45, A.46, I.47, F.48, T.92, P.93, H.94 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:Y.18, E:Y.18, E:F.48 Hydrogen bonds: E:Q.16, E:I.47, E:H.94, D:Q.3, D:Q.3, E:Y.18, E:Y.18, E:G.45 Water bridges: E:T.19, E:G.45

1 x BGC- GAL- FUC- A2G- FUC: alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]beta-D-glucopyranose(Non-covalent)

BGC-GAL-FUC-A2G-FUC.2: 12 residues within 4Å: Chain C: Q.3 Chain D: Q.16, I.17, Y.18, N.44, G.45, A.46, I.47, F.48, P.93, H.94 Ligands: GLC.21 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:Q.16, D:Y.18, D:Y.18, D:A.46, D:F.48 Hydrogen bonds: D:I.47, D:H.94, C:Q.3, C:Q.3, D:Y.18, D:Y.18 Water bridges: D:T.92, C:Q.3, C:Q.3

10 x CA: CALCIUM ION(Non-covalent)

CA.4: 3 residues within 4Å: Chain A: E.79 Ligands: BCN.5, CA.6 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.79, A:E.79 CA.6: 4 residues within 4Å: Chain A: E.79 Chain E: N.103 Ligands: CA.4, BCN.7 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.79 CA.9: 3 residues within 4Å: Chain B: E.79 Ligands: BCN.11, CA.12 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.79, B:E.79 CA.12: 3 residues within 4Å: Chain B: E.79 Ligands: BCN.8, CA.9 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.79 CA.13: 3 residues within 4Å: Chain C: E.79 Ligands: BCN.15, CA.16 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.79, C:E.79, H2O.10 CA.16: 3 residues within 4Å: Chain C: E.79 Ligands: CA.13, BCN.14 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.79, H2O.6 CA.17: 4 residues within 4Å: Chain D: K.23, E.79 Ligands: BCN.19, CA.20 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.79, D:E.79, H2O.11 CA.20: 4 residues within 4Å: Chain C: N.103 Chain D: E.79 Ligands: CA.17, BCN.18 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.79 CA.23: 3 residues within 4Å: Chain E: E.79 Ligands: BCN.24, CA.25 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.79, E:E.79, H2O.18 CA.25: 3 residues within 4Å: Chain E: E.79 Ligands: BCN.22, CA.23 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:E.79

10 x BCN: BICINE(Non-covalent)

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

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

FUC.10: 8 residues within 4Å: Chain A: Q.3 Chain B: Y.18, A.46, I.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:Y.18, B:F.48 Hydrogen bonds: B:I.47, B:H.94, A:Q.3, A:Q.3 Water bridges: A:Q.3

1 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.21: 7 residues within 4Å: Chain D: N.44, G.45, I.47 Ligands: BGC-GAL-FUC-A2G-FUC.2, BGC-GAL-FUC-A2G-FUC.2, BGC-GAL-FUC-A2G-FUC.2, BGC-GAL-FUC-A2G-FUC.2 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.45

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Heggelund, J.E. et al., High-Resolution Crystal Structures Elucidate the Molecular Basis of Cholera Blood Group Dependence. Plos Pathog. (2016)

Release Date

2016-03-30

Peptides

Cholera enterotoxin subunit B: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Cholera enterotoxin subunit B

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