SMTL ID : 5elb.2 (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

3 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

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, A:H.94, E:Q.3, E:Q.3, A:G.45, A:G.45 Water bridges: A:H.94 NDG-GAL-FUC-FUC.2: 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:H.94, A:Q.3, A:Q.3, B:G.45, B:G.45 Water bridges: B:Q.16, B:Q.16, B:Q.16, B:H.94 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: 4 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:F.48 Hydrogen bonds: C:T.47, C:H.94, C:H.94, B:Q.3, C:Q.16, C:G.45, C:G.45 Water bridges: C:H.94, C:T.47, C:T.47

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

NAG-FUC-NDG-GAL-FUC.4: 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 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:A.46 Water bridges: D:N.44, D:N.44, D:H.94, C:Q.3 Hydrogen bonds: D:Q.16, D:G.45, D:G.45, C:Q.3, D:G.45 NAG-FUC-NDG-GAL-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 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:A.46 Hydrogen bonds: E:N.44, E:Q.16, E:H.18, E:G.45, E:G.45, E:G.45, D:Q.3 Water bridges: D:Q.3

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

GLA.6: 9 residues within 4Å: Chain A: N.14, E.51, Q.56, H.57, Q.61, W.88, N.90, K.91 Ligands: GAL.7 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.14, A:N.14, A:Q.56, A:Q.61, A:N.90, A:N.90, A:K.91 Water bridges: A:E.51 GLA.9: 8 residues within 4Å: Chain B: E.51, Q.56, H.57, Q.61, W.88, N.90, K.91 Ligands: GAL.10 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.61, B:Q.61, B:N.90, B:N.90, B:K.91 Water bridges: B:E.51, B:I.58 GLA.12: 8 residues within 4Å: Chain C: E.51, Q.56, H.57, Q.61, W.88, N.90, K.91 Ligands: GAL.11 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Q.61, C:N.90, C:N.90, C:K.91 Water bridges: C:E.51, C:I.58 GLA.14: 8 residues within 4Å: Chain D: E.51, Q.56, H.57, Q.61, W.88, N.90, K.91 Ligands: GAL.13 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:Q.61, D:Q.61, D:N.90, D:N.90, D:K.91 Water bridges: D:E.51, D:I.58, D:K.91, D:K.91 GLA.16: 8 residues within 4Å: Chain E: E.51, Q.56, H.57, Q.61, W.88, N.90, K.91 Ligands: GAL.15 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:Q.56, E:Q.61, E:Q.61, E:N.90, E:N.90, E:K.91 Water bridges: E:E.51 Salt bridges: E:K.91

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

GAL.7: 9 residues within 4Å: Chain A: N.14, E.51, Q.56, H.57, Q.61, W.88, N.90, K.91 Ligands: GLA.6 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.14, A:Q.61, A:N.90, A:N.90, A:K.91 Salt bridges: A:K.91 GAL.10: 8 residues within 4Å: Chain B: E.51, Q.56, H.57, Q.61, W.88, N.90, K.91 Ligands: GLA.9 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Q.61, B:Q.61, B:N.90, B:N.90, B:K.91 Water bridges: B:E.51, B:I.58 Salt bridges: B:K.91 GAL.11: 8 residues within 4Å: Chain C: E.51, Q.56, H.57, Q.61, W.88, N.90, K.91 Ligands: GLA.12 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Q.61, C:N.90, C:N.90, C:K.91 Water bridges: C:E.51, C:I.58 Salt bridges: C:K.91 GAL.13: 8 residues within 4Å: Chain D: E.51, Q.56, H.57, Q.61, W.88, N.90, K.91 Ligands: GLA.14 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:Q.61, D:Q.61, D:N.90, D:N.90, D:K.91 Water bridges: D:E.51, D:I.58, D:K.91 GAL.15: 8 residues within 4Å: Chain E: E.51, Q.56, H.57, Q.61, W.88, N.90, K.91 Ligands: GLA.16 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:Q.56, E:Q.61, E:Q.61, E:N.90, E:N.90, E:K.91 Water bridges: E:E.51 Salt bridges: E:K.91

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 3 residues within 4Å: Chain B: T.6, E.83, K.84 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.6, B:E.83

Links

RCSB   PDBe   PDBe-KB   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
F

B
G

C
H

D
I

E
J

Cholera enterotoxin B subunit

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