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

Cholera toxin El Tor B-pentamer in complex with A Lewis-y

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-pentamer

Ligands

1 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(Non-covalent)

NDG-GAL-FUC-A2G-FUC.1: 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, T.92, P.93, H.94 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:Q.16, D:F.48, D:I.47 Hydrogen bonds: C:Q.3, C:Q.3, D:I.47, D:H.94, D:Y.18, D:Y.18, D:G.45, D:G.45

10 x CA: CALCIUM ION(Non-covalent)

CA.2: 3 residues within 4Å: Chain A: E.79 Ligands: CA.5, BCN.6 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.79, A:E.79, H2O.1 CA.5: 3 residues within 4Å: Chain A: E.79 Ligands: CA.2, BCN.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.79 CA.8: 3 residues within 4Å: Chain B: E.79 Ligands: BCN.9, CA.10 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.79, B:E.79, H2O.4 CA.10: 3 residues within 4Å: Chain B: E.79 Ligands: BCN.7, CA.8 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.79, H2O.2 CA.12: 4 residues within 4Å: Chain C: K.23, E.79 Ligands: BCN.13, CA.14 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.79, C:E.79, H2O.6 CA.14: 3 residues within 4Å: Chain C: E.79 Ligands: BCN.11, CA.12 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.79, H2O.9 CA.16: 3 residues within 4Å: Chain D: E.79 Ligands: BCN.17, CA.18 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.79, D:E.79 CA.18: 3 residues within 4Å: Chain D: E.79 Ligands: BCN.15, CA.16 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.79, H2O.12 CA.20: 3 residues within 4Å: Chain E: E.79 Ligands: BCN.21, CA.22 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:E.79, E:E.79 CA.22: 3 residues within 4Å: Chain E: E.79 Ligands: BCN.19, CA.20 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.79, H2O.16

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

FUC.3: 9 residues within 4Å: Chain A: Y.18, G.45, A.46, I.47, F.48, T.92, P.93, H.94 Chain E: Q.3 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: A:Y.18, A:F.48 Hydrogen bonds: A:I.47, A:H.94, E:Q.3, E:Q.3

10 x BCN: BICINE(Non-covalent)

BCN.4: 8 residues within 4Å: Chain A: Y.76, L.77, E.79 Chain E: A.80, K.81, N.103 Ligands: CA.5, BCN.6 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:K.81, E:N.103 Water bridges: E:K.81, E:A.102 Salt bridges: A:E.79 BCN.6: 3 residues within 4Å: Chain A: E.79 Ligands: CA.2, BCN.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.79 Salt bridges: A:K.23, A:E.79 BCN.7: 8 residues within 4Å: Chain A: A.80, K.81, N.103 Chain B: Y.76, L.77, E.79 Ligands: BCN.9, CA.10 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.9: 3 residues within 4Å: Chain B: E.79 Ligands: BCN.7, CA.8 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.23, B:E.79 BCN.11: 8 residues within 4Å: Chain B: A.80, K.81, N.103 Chain C: Y.76, L.77, E.79 Ligands: BCN.13, CA.14 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:K.81, B:N.103 Water bridges: B:K.81, B:A.102, B:N.103, B:N.103, C:E.79 Salt bridges: C:E.79 BCN.13: 4 residues within 4Å: Chain C: K.23, E.79 Ligands: BCN.11, CA.12 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.79 Salt bridges: C:K.23, C:E.79 BCN.15: 8 residues within 4Å: Chain C: A.80, K.81, N.103 Chain D: Y.76, L.77, E.79 Ligands: BCN.17, CA.18 7 PLIP interactions: 1 interactions with chain D, 6 interactions with chain C Salt bridges: D:E.79 Hydrogen bonds: C:K.81, C:N.103 Water bridges: C:K.81, C:A.102, C:N.103, C:N.103 BCN.17: 3 residues within 4Å: Chain D: E.79 Ligands: BCN.15, CA.16 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:E.79 Water bridges: D:K.23, D:E.79 Salt bridges: D:K.23, D:E.79 BCN.19: 8 residues within 4Å: Chain D: A.80, K.81, N.103 Chain E: Y.76, L.77, E.79 Ligands: BCN.21, CA.22 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain E Hydrogen bonds: D:K.81, D:N.103, E:K.23, E:K.23 Water bridges: E:E.79 Salt bridges: E:E.79 BCN.21: 3 residues within 4Å: Chain E: E.79 Ligands: BCN.19, CA.20 1 PLIP interactions: 1 interactions with chain E Salt bridges: 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 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

Related Entries With Identical Sequence