SMTL ID : 5eld.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-pentamer

Ligands

4 x NDG- 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)]2-acetamido-2-deoxy-alpha-D-glucopyranose

NDG-GAL-FUC-A2G-FUC.1: 14 residues within 4Å: Chain A: Q.16, I.17, H.18, N.44, G.45, A.46, T.47, F.48, K.91, T.92, P.93, H.94 Chain E: Q.3 Ligands: PEG.5 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain E Water bridges: A:H.18, A:T.92 Hydrophobic interactions: A:F.48 Hydrogen bonds: A:T.47, A:H.94, A:H.94, E:Q.3, E:Q.3, A:Q.16, A:H.18, A:G.45, A:G.45, E:Q.3 NDG-GAL-FUC-A2G-FUC.2: 13 residues within 4Å: Chain B: Q.3 Chain C: Q.16, I.17, H.18, N.44, G.45, A.46, T.47, F.48, T.92, P.93, H.94 Ligands: PGE.9 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:Q.3, B:Q.3, B:Q.3, C:T.47, C:H.94, C:H.94, C:Q.16, C:G.45, C:G.45 Hydrophobic interactions: C:F.48 Water bridges: C:H.94 NDG-GAL-FUC-A2G-FUC.3: 12 residues within 4Å: Chain C: Q.3 Chain D: Q.16, I.17, 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 Water bridges: D:H.18, D:H.18 Hydrophobic interactions: D:F.48 Hydrogen bonds: D:T.47, D:H.94, C:Q.3, C:Q.3, D:Q.16, D:H.18, D:G.45, D:G.45 NDG-GAL-FUC-A2G-FUC.4: 12 residues within 4Å: Chain D: Q.3 Chain E: Q.16, I.17, H.18, N.44, G.45, A.46, T.47, F.48, P.93, H.94 Ligands: PGE.13 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:F.48 Hydrogen bonds: E:T.47, E:H.94, D:Q.3, E:Q.16, E:G.45, E:G.45

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

PEG.5: 5 residues within 4Å: Chain A: F.25, F.42, K.43, G.45 Ligands: NDG-GAL-FUC-A2G-FUC.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.43 PEG.11: 4 residues within 4Å: Chain D: E.11, Y.12 Chain E: K.34, R.35 No protein-ligand interaction detected (PLIP)

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

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

1 x NA: SODIUM ION(Non-functional Binders)

NA.7: 4 residues within 4Å: Chain B: C.9, A.10, Y.12, T.15 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.12, B:T.15, B:T.15

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.8: 6 residues within 4Å: Chain A: T.78 Chain B: I.74, L.77, T.78 Chain C: I.74, T.78 No protein-ligand interaction detected (PLIP)

3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.9: 6 residues within 4Å: Chain C: F.25, T.41, F.42, K.43, G.45 Ligands: NDG-GAL-FUC-A2G-FUC.2 No protein-ligand interaction detected (PLIP) PGE.12: 5 residues within 4Å: Chain D: F.25, T.41, F.42, K.43, G.45 No protein-ligand interaction detected (PLIP) PGE.13: 6 residues within 4Å: Chain E: F.25, T.41, F.42, K.43, G.45 Ligands: NDG-GAL-FUC-A2G-FUC.4 No protein-ligand interaction detected (PLIP)

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

GLA.15: 8 residues within 4Å: Chain E: E.51, Q.56, H.57, Q.61, W.88, N.90, K.91 Ligands: GAL.14 9 PLIP interactions: 9 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:W.88, E:K.91, E:K.91

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
A

B
B

C
C

D
D

E
E

Cholera enterotoxin B subunit

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