SMTL ID : 3dwq.1

Crystal structure of the A-subunit of the AB5 toxin from E. coli with Neu5Gc-2,3Gal-1,3GlcNAc

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-pentamer

Ligands

4 x NGA- GAL- NGC: N-glycolyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose

NGA-GAL-NGC.1: 11 residues within 4Å: Chain A: G.9, M.10, F.11, S.12, Q.36, S.40, Y.78, T.107, E.108 Ligands: POL.5, AZI.6 13 PLIP interactions: 13 interactions with chain A Water bridges: A:S.12, A:S.12, A:S.12, A:Y.78 Hydrogen bonds: A:E.108, A:D.8, A:M.10, A:M.10, A:S.12, A:Q.36, A:Q.36, A:S.40, A:S.40, A:Y.78, A:R.114 NGA-GAL-NGC.2: 12 residues within 4Å: Chain C: D.8, G.9, M.10, F.11, S.12, Q.36, S.40, Y.78, T.107, K.115 Ligands: POL.9, AZI.10 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:T.107, C:K.115, C:K.115, C:M.10, C:M.10, C:S.12, C:Q.36, C:Q.36, C:S.40, C:S.40, C:Y.78 Water bridges: C:Q.36, C:T.107, C:T.107 NGA-GAL-NGC.3: 11 residues within 4Å: Chain D: G.9, M.10, F.11, S.12, Q.36, Y.78, T.107, E.108, K.115 Ligands: POL.11, AZI.12 10 PLIP interactions: 10 interactions with chain D Water bridges: D:S.12, D:S.12, D:S.12 Hydrogen bonds: D:M.10, D:M.10, D:S.12, D:Q.36, D:Q.36, D:S.40, D:S.40, D:Y.78 NGA-GAL-NGC.4: 11 residues within 4Å: Chain E: D.8, G.9, M.10, F.11, S.12, Q.36, S.40, Y.78, T.107, K.115 Ligands: POL.15 11 PLIP interactions: 11 interactions with chain E Water bridges: E:S.12, E:K.115, E:K.115, E:S.12, E:S.12 Hydrogen bonds: E:D.8, E:M.10, E:M.10, E:S.12, E:Q.36, E:Q.36, E:S.40, E:S.40, E:Y.78

4 x POL: N-PROPANOL(Non-functional Binders)

POL.5: 2 residues within 4Å: Ligands: NGA-GAL-NGC.1, AZI.6 No protein-ligand interaction detected (PLIP) POL.9: 2 residues within 4Å: Ligands: NGA-GAL-NGC.2, AZI.10 No protein-ligand interaction detected (PLIP) POL.11: 2 residues within 4Å: Ligands: NGA-GAL-NGC.3, AZI.12 No protein-ligand interaction detected (PLIP) POL.15: 2 residues within 4Å: Ligands: NGA-GAL-NGC.4, AZI.16 No protein-ligand interaction detected (PLIP)

4 x AZI: AZIDE ION(Non-covalent)(Non-functional Binders)

AZI.6: 3 residues within 4Å: Chain A: E.108 Ligands: NGA-GAL-NGC.1, POL.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.108 AZI.10: 2 residues within 4Å: Ligands: NGA-GAL-NGC.2, POL.9 No protein-ligand interaction detected (PLIP) AZI.12: 2 residues within 4Å: Ligands: NGA-GAL-NGC.3, POL.11 No protein-ligand interaction detected (PLIP) AZI.16: 2 residues within 4Å: Chain E: E.108 Ligands: POL.15 No protein-ligand interaction detected (PLIP)

5 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.7: 7 residues within 4Å: Chain A: L.65, Y.66, T.69, T.70 Chain C: Y.68, T.69 Ligands: 1PE.14 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Water bridges: A:N.62 Hydrogen bonds: C:Y.68 1PE.8: 7 residues within 4Å: Chain B: N.62, L.65, Y.66, T.69, T.70 Chain E: T.69 Ligands: 1PE.17 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.62 1PE.13: 7 residues within 4Å: Chain B: Y.68, T.69 Chain D: N.62, Y.66, T.69, T.70 Ligands: 1PE.14 1 PLIP interactions: 1 interactions with chain D Water bridges: D:N.62 1PE.14: 7 residues within 4Å: Chain C: N.62, Y.66, T.69 Chain D: Y.61, L.65 Ligands: 1PE.7, 1PE.13 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.62 1PE.17: 5 residues within 4Å: Chain A: T.69 Chain E: Y.66, T.69, T.70 Ligands: 1PE.8 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Byres, E. et al., Incorporation of a non-human glycan mediates human susceptibility to a bacterial toxin. Nature (2008)

Release Date

2008-11-04

Peptides

Subtilase cytotoxin, subunit B: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Subtilase cytotoxin, subunit B

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