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

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.08 Å

Oligo State

homo-pentamer

Ligands

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

NDG-GAL-FUC-FUC.1: 10 residues within 4Å: Chain A: H.18, N.44, G.45, A.46, T.47, F.48, T.92, P.93, H.94 Chain E: Q.3 4 PLIP interactions: 2 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, A:H.94, A:G.45, A:G.45 Water bridges: A:Q.16, A:Q.16, A:Q.16 NDG-GAL-FUC-FUC.2: 10 residues within 4Å: Chain A: Q.3 Chain B: 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:H.94, A:Q.3, A:Q.3, B:H.94, B:G.45, B:G.45 Water bridges: B:Q.16, B:Q.16 NDG-GAL-FUC-FUC.3: 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.18, C:G.45, C:G.45 Water bridges: B:Q.3 NDG-GAL-FUC-FUC.4: 10 residues within 4Å: Chain C: Q.3 Chain D: 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 D, 2 interactions with chain C Hydrophobic interactions: D:F.48 Hydrogen bonds: D:T.47, D:H.94, C:Q.3, C:Q.3, D:G.45, D:G.45 Water bridges: D:H.94 NDG-GAL-FUC-FUC.5: 11 residues within 4Å: Chain D: Q.3 Chain E: 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 E, 2 interactions with chain D Hydrophobic interactions: E:F.48 Hydrogen bonds: E:T.47, E:H.94, D:Q.3, E:Q.16, E:H.94, E:G.45, E:G.45 Water bridges: D:Q.3, E:H.94

10 x CA: CALCIUM ION(Non-covalent)

CA.6: 3 residues within 4Å: Chain A: E.79 Ligands: BCN.9, CA.10 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.79, A:E.79, H2O.5 CA.10: 3 residues within 4Å: Chain A: E.79 Ligands: CA.6, BCN.11 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.79, H2O.5 CA.12: 3 residues within 4Å: Chain B: E.79 Ligands: BCN.13, CA.16 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.79, B:E.79 CA.16: 3 residues within 4Å: Chain B: E.79 Ligands: CA.12, BCN.17 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.79, H2O.11 CA.18: 3 residues within 4Å: Chain C: E.79 Ligands: CA.21, BCN.23 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.79, C:E.79 CA.21: 3 residues within 4Å: Chain C: E.79 Ligands: CA.18, BCN.22 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.79, H2O.18 CA.25: 3 residues within 4Å: Chain D: E.79 Ligands: BCN.26, CA.29 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.79, D:E.79, H2O.23 CA.29: 3 residues within 4Å: Chain D: E.79 Ligands: BCN.24, CA.25 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.79, H2O.15 CA.31: 3 residues within 4Å: Chain E: E.79 Ligands: BCN.32, CA.35 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.79, E:E.79, H2O.25 CA.35: 3 residues within 4Å: Chain E: E.79 Ligands: BCN.30, CA.31 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.79, H2O.22

5 x GAL: beta-D-galactopyranose(Non-covalent)

GAL.7: 8 residues within 4Å: Chain A: E.51, Q.56, H.57, Q.61, W.88, N.90, K.91 Ligands: GLA.8 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.61, A:N.90, A:N.90, A:K.91 Water bridges: A:I.58 GAL.14: 8 residues within 4Å: Chain B: E.51, Q.56, H.57, Q.61, W.88, N.90, K.91 Ligands: GLA.15 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.56, B:Q.61, B:N.90, B:N.90, B:K.91 Water bridges: B:I.58 GAL.19: 8 residues within 4Å: Chain C: E.51, Q.56, H.57, Q.61, W.88, N.90, K.91 Ligands: GLA.20 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:Q.56, C:Q.61, C:Q.61, C:N.90, C:N.90, C:K.91 Water bridges: C:I.58 Salt bridges: C:K.91 GAL.27: 8 residues within 4Å: Chain D: E.51, Q.56, H.57, Q.61, W.88, N.90, K.91 Ligands: GLA.28 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:Q.61, D:Q.61, D:N.90, D:N.90, D:K.91 Salt bridges: D:K.91 GAL.33: 8 residues within 4Å: Chain E: E.51, Q.56, H.57, Q.61, W.88, N.90, K.91 Ligands: GLA.34 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:Q.61, E:Q.61, E:N.90, E:N.90, E:K.91 Salt bridges: E:K.91

5 x GLA: alpha-D-galactopyranose(Non-covalent)

GLA.8: 8 residues within 4Å: Chain A: E.51, Q.56, H.57, Q.61, W.88, N.90, K.91 Ligands: GAL.7 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.61, A:Q.61, A:N.90, A:N.90, A:K.91 Water bridges: A:I.58 Salt bridges: A:K.91 GLA.15: 8 residues within 4Å: Chain B: E.51, Q.56, H.57, Q.61, W.88, N.90, K.91 Ligands: GAL.14 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.61, B:N.90, B:N.90, B:K.91 Water bridges: B:I.58 GLA.20: 8 residues within 4Å: Chain C: E.51, Q.56, H.57, Q.61, W.88, N.90, K.91 Ligands: GAL.19 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:Q.56, C:Q.61, C:Q.61, C:N.90, C:N.90, C:K.91 Water bridges: C:N.14, C:I.58 GLA.28: 8 residues within 4Å: Chain D: E.51, Q.56, H.57, Q.61, W.88, N.90, K.91 Ligands: GAL.27 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.61, D:Q.61, D:N.90, D:N.90, D:K.91 GLA.34: 8 residues within 4Å: Chain E: E.51, Q.56, H.57, Q.61, W.88, N.90, K.91 Ligands: GAL.33 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:Q.61, E:Q.61, E:N.90, E:N.90, E:K.91

10 x BCN: BICINE(Non-covalent)

BCN.9: 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.11: 7 residues within 4Å: Chain A: Y.76, L.77, E.79 Chain E: A.80, K.81, N.103 Ligands: CA.10 8 PLIP interactions: 2 interactions with chain E, 6 interactions with chain A Hydrogen bonds: E:K.81, E:N.103, A:E.79 Water bridges: A:Y.76, A:Y.76, A:E.79, A:E.79 Salt bridges: A:E.79 BCN.13: 3 residues within 4Å: Chain B: K.23, E.79 Ligands: CA.12 4 PLIP interactions: 4 interactions with chain B Water bridges: B:K.23, B:K.23 Salt bridges: B:K.23, B:E.79 BCN.17: 7 residues within 4Å: Chain A: A.80, K.81, N.103 Chain B: Y.76, L.77, E.79 Ligands: CA.16 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.81, A:N.103, A:N.103, B:E.79 Salt bridges: B:E.79 BCN.22: 7 residues within 4Å: Chain B: A.80, K.81, N.103 Chain C: Y.76, L.77, E.79 Ligands: CA.21 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:K.81, B:N.103, C:E.79 Water bridges: C:E.79 Salt bridges: C:E.79 BCN.23: 2 residues within 4Å: Chain C: E.79 Ligands: CA.18 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.79, C:E.79 Salt bridges: C:E.79 BCN.24: 7 residues within 4Å: Chain C: A.80, K.81, N.103 Chain D: Y.76, L.77, E.79 Ligands: CA.29 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:K.81, C:N.103, D:E.79 Water bridges: C:K.23, D:E.79 Salt bridges: C:K.23, D:E.79 BCN.26: 3 residues within 4Å: Chain D: K.23, E.79 Ligands: CA.25 4 PLIP interactions: 4 interactions with chain D Water bridges: D:K.23, D:K.23 Salt bridges: D:K.23, D:E.79 BCN.30: 7 residues within 4Å: Chain D: A.80, K.81, N.103 Chain E: Y.76, L.77, E.79 Ligands: CA.35 6 PLIP interactions: 3 interactions with chain E, 3 interactions with chain D Hydrogen bonds: E:E.79, D:K.81, D:N.103, D:N.103 Water bridges: E:K.23 Salt bridges: E:E.79 BCN.32: 2 residues within 4Å: Chain E: E.79 Ligands: CA.31 2 PLIP interactions: 2 interactions with chain E Salt bridges: E:K.23, E:E.79

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 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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