SMTL ID : 3chb.1

CHOLERA TOXIN B-PENTAMER COMPLEXED WITH GM1 PENTASACCHARIDE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

homo-pentamer

Ligands

2 x GAL- NGA- GAL- SIA: beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose

GAL-NGA-GAL-SIA.1: 14 residues within 4Å: Chain A: E.12, Y.13, H.14, E.52, Q.57, H.58, I.59, Q.62, W.89, N.91, K.92 Chain B: G.34, K.35 Ligands: GLC.6 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.62, A:Q.62, A:N.91, A:N.91, A:K.92, B:G.34, A:E.12, A:H.14 Water bridges: A:E.52, A:H.14, A:N.91, A:N.91, A:E.12, A:Q.62 Hydrophobic interactions: A:H.14, A:E.12, A:Y.13 GAL-NGA-GAL-SIA.3: 15 residues within 4Å: Chain C: E.12, Y.13, H.14, N.15, E.52, Q.57, H.58, I.59, Q.62, W.89, N.91, K.92 Chain D: G.34, K.35 Ligands: GLC.9 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:Q.62, C:Q.62, C:N.91, C:N.91, C:K.92, C:I.59, C:E.12, C:H.14, C:Q.62 Water bridges: C:E.52, C:H.14, C:N.91, C:N.91, C:E.12, C:H.14, C:Q.62, C:Q.62, D:G.34 Hydrophobic interactions: C:H.14, C:E.12 Salt bridges: C:H.14

3 x BGC- GAL- NGA- GAL- SIA: beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranose(Non-functional Binders)

BGC-GAL-NGA-GAL-SIA.2: 14 residues within 4Å: Chain B: E.12, Y.13, H.14, E.52, Q.57, H.58, I.59, Q.62, W.89, N.91, K.92 Chain C: G.34, K.35, R.36 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.62, B:Q.62, B:N.91, B:N.91, B:K.92, B:E.12, B:H.14 Hydrophobic interactions: B:H.14 Water bridges: B:H.14, B:E.12, B:I.59, B:Q.62, B:Q.62 Salt bridges: B:H.14 BGC-GAL-NGA-GAL-SIA.4: 13 residues within 4Å: Chain D: E.12, Y.13, H.14, N.15, E.52, Q.57, H.58, I.59, Q.62, W.89, N.91, K.92 Chain E: G.34 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.62, D:Q.62, D:N.91, D:N.91, D:K.92, D:S.56, D:E.12, D:H.14, D:H.14 Water bridges: D:E.52, D:I.59, D:I.59, D:N.91, D:E.12, D:H.14, D:I.59, D:Q.62 Salt bridges: D:H.14 BGC-GAL-NGA-GAL-SIA.5: 13 residues within 4Å: Chain A: G.34 Chain E: E.12, Y.13, H.14, N.15, E.52, Q.57, H.58, I.59, Q.62, W.89, N.91, K.92 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Q.62, E:Q.62, E:N.91, E:N.91, E:K.92, E:E.12, E:H.14, E:H.14 Hydrophobic interactions: E:H.14 Water bridges: E:N.91, E:N.91, E:I.59, E:Q.62 Salt bridges: E:H.14

2 x GLC: alpha-D-glucopyranose(Non-functional Binders)

GLC.6: 1 residues within 4Å: Ligands: GAL-NGA-GAL-SIA.1 No protein-ligand interaction detected (PLIP) GLC.9: 1 residues within 4Å: Ligands: GAL-NGA-GAL-SIA.3 No protein-ligand interaction detected (PLIP)

5 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.7: 4 residues within 4Å: Chain A: C.10, A.11, T.16, Q.17 No protein-ligand interaction detected (PLIP) UNX.8: 3 residues within 4Å: Chain B: C.10, A.11, T.16 No protein-ligand interaction detected (PLIP) UNX.10: 4 residues within 4Å: Chain C: C.10, A.11, T.16, Q.17 No protein-ligand interaction detected (PLIP) UNX.11: 3 residues within 4Å: Chain D: C.10, A.11, T.16 No protein-ligand interaction detected (PLIP) UNX.14: 3 residues within 4Å: Chain E: C.10, A.11, T.16 No protein-ligand interaction detected (PLIP)

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

MES.12: 5 residues within 4Å: Chain D: N.90, N.91, K.92, T.93, R.95 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.93 Salt bridges: D:R.95 MES.13: 1 residues within 4Å: Chain D: K.44 2 PLIP interactions: 2 interactions with chain D Water bridges: D:K.44 Salt bridges: D:K.44

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Merritt, E.A. et al., The 1.25 A resolution refinement of the cholera toxin B-pentamer: evidence of peptide backbone strain at the receptor-binding site. J.Mol.Biol. (1998)

Release Date

1998-08-12

Peptides

CHOLERA TOXIN: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

D
G

E
H

CHOLERA TOXIN