SMTL ID : 1bos.1 (3 other biounits)

SHIGA-LIKE TOXIN COMPLEXED WITH ITS RECEPTOR

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-pentamer

Ligands

8 x BGC- GAL- GLA: alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose

BGC-GAL-GLA.1: 10 residues within 4Å: Chain A: T.1, T.31, N.32, R.33, T.54, N.55, G.62, F.63, S.64 Chain B: D.16 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.55, A:G.62, A:N.32, A:N.32, A:R.33, A:R.33, A:F.63 Water bridges: A:E.65, A:S.64, B:D.16 BGC-GAL-GLA.3: 8 residues within 4Å: Chain A: K.13, N.15, D.17, T.19, T.21, E.28, F.30, G.60 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.17, A:G.60, A:T.21, A:E.28, A:E.28, A:G.60 BGC-GAL-GLA.4: 11 residues within 4Å: Chain B: T.1, F.30, T.31, N.32, R.33, T.54, N.55, G.62, F.63, S.64 Chain C: D.16 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.55, B:F.30, B:N.32, B:N.32, B:R.33, B:R.33, B:F.63, B:S.64, B:S.64 Water bridges: B:T.1, B:T.1, B:G.62 BGC-GAL-GLA.7: 10 residues within 4Å: Chain C: T.1, T.31, N.32, R.33, T.54, N.55, G.62, F.63, S.64 Chain D: D.16 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.55, C:N.32, C:N.32, C:R.33, C:R.33, C:F.63, C:S.64, C:S.64 Water bridges: C:G.62, C:G.62 BGC-GAL-GLA.9: 11 residues within 4Å: Chain D: T.1, F.30, T.31, N.32, R.33, T.54, N.55, G.62, F.63, S.64 Chain E: D.16 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain E Water bridges: D:N.55, D:T.1, D:N.55, E:D.16 Hydrogen bonds: D:T.54, D:N.55, E:D.16, D:F.30, D:N.32, D:N.32, D:R.33, D:R.33, D:F.63 BGC-GAL-GLA.11: 7 residues within 4Å: Chain D: N.15, D.17, T.19, T.21, E.28, F.30, G.60 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.17, D:E.28, D:E.28 BGC-GAL-GLA.12: 10 residues within 4Å: Chain A: D.16 Chain E: T.1, T.31, N.32, R.33, T.54, N.55, G.62, F.63, S.64 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:N.55, E:N.32, E:N.32, E:R.33, E:R.33, E:F.63, E:S.64, E:S.64 Water bridges: E:T.1, E:G.62 BGC-GAL-GLA.13: 7 residues within 4Å: Chain A: Y.14, D.18, W.34 Chain E: N.32, R.33, W.34, N.35 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain A Water bridges: E:N.32, E:W.34 Hydrogen bonds: E:W.34, E:N.35, E:N.35, A:D.18

5 x GAL- GLA: alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose(Non-covalent)

GAL-GLA.2: 7 residues within 4Å: Chain A: N.32, R.33, W.34, N.35 Chain B: Y.14, D.18, W.34 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:W.34, A:N.35, A:N.35, B:Y.14, B:D.18 GAL-GLA.5: 7 residues within 4Å: Chain B: N.32, R.33, W.34, N.35 Chain C: Y.14, D.18, W.34 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:N.32, B:W.34, B:N.35, C:Y.14, C:D.18 GAL-GLA.6: 8 residues within 4Å: Chain B: K.13, N.15, D.17, T.19, T.21, E.28, F.30, G.60 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.17, B:T.21, B:E.28, B:E.28 GAL-GLA.8: 6 residues within 4Å: Chain C: N.32, R.33, W.34, N.35 Chain D: D.18, W.34 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:R.33, C:W.34, C:N.35, C:N.35 Water bridges: D:D.18, D:D.18 GAL-GLA.10: 6 residues within 4Å: Chain D: N.32, R.33, W.34, N.35 Chain E: D.18, W.34 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:W.34, D:N.35, D:N.35, E:D.18

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

GAL.14: 5 residues within 4Å: Chain C: K.13, N.15, T.21, E.28, G.60 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.28, C:E.28 Water bridges: C:K.13 GAL.15: 3 residues within 4Å: Chain E: T.21, E.28, G.60 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:T.21, E:E.28, E:E.28, E:G.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ling, H. et al., Structure of the shiga-like toxin I B-pentamer complexed with an analogue of its receptor Gb3. Biochemistry (1998)

Release Date

1999-02-02

Peptides

SHIGA-LIKE TOXIN I B SUBUNIT: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

SHIGA-LIKE TOXIN I B SUBUNIT

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