SMTL ID : 1qnu.1

Shiga-Like Toxin I B Subunit Complexed with the Bridged-Starfish Inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.23 Å

Oligo State

homo-10-mer

Ligands

10 x GLC- GAL- GAL: beta-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose

GLC-GAL-GAL.1: 13 residues within 4Å: Chain A: T.1, T.31, N.32, R.33, T.54, N.55, A.56, G.62, F.63, S.64 Chain B: D.16 Ligands: EMB.6, MEC.7 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:F.30, A:T.31, A:N.32, A:N.32, A:R.33, A:R.33, A:F.63, A:S.64, A:S.64 Water bridges: B:D.16 GLC-GAL-GAL.2: 14 residues within 4Å: Chain B: T.1, F.30, T.31, N.32, R.33, T.54, N.55, A.56, G.62, F.63, S.64 Chain C: D.16 Ligands: EMB.8, MEC.9 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:F.30, B:T.31, B:N.32, B:N.32, B:R.33, B:R.33, B:F.63, B:S.64, B:S.64 Water bridges: C:D.16 GLC-GAL-GAL.3: 13 residues within 4Å: Chain C: T.1, T.31, N.32, R.33, T.54, N.55, A.56, G.62, F.63, S.64 Chain D: D.16 Ligands: EMB.10, MEC.11 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:F.30, C:T.31, C:N.32, C:N.32, C:R.33, C:R.33, C:F.63, C:S.64, C:S.64, D:D.16 GLC-GAL-GAL.4: 13 residues within 4Å: Chain D: T.1, T.31, N.32, R.33, T.54, N.55, A.56, G.62, F.63, S.64 Chain E: D.16 Ligands: EMB.12, MEC.13 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:F.30, D:T.31, D:N.32, D:N.32, D:R.33, D:R.33, D:F.63, D:S.64, D:S.64, E:D.16 Water bridges: E:D.16 GLC-GAL-GAL.5: 13 residues within 4Å: Chain A: D.16 Chain E: T.1, T.31, N.32, R.33, T.54, N.55, A.56, G.62, F.63, S.64 Ligands: EMB.14, MEC.15 10 PLIP interactions: 9 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:T.31, E:T.31, E:N.32, E:N.32, E:R.33, E:R.33, E:F.63, E:S.64, E:S.64 Water bridges: A:D.16 GLC-GAL-GAL.16: 13 residues within 4Å: Chain F: T.1, T.31, N.32, R.33, T.54, N.55, A.56, G.62, F.63, S.64 Chain G: D.16 Ligands: EMB.21, MEC.22 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:F.30, F:N.32, F:N.32, F:R.33, F:R.33, F:F.63, F:S.64, F:S.64 GLC-GAL-GAL.17: 14 residues within 4Å: Chain G: T.1, F.30, T.31, N.32, R.33, T.54, N.55, A.56, G.62, F.63, S.64 Chain H: D.16 Ligands: EMB.23, MEC.24 8 PLIP interactions: 8 interactions with chain G Hydrogen bonds: G:F.30, G:N.32, G:N.32, G:R.33, G:R.33, G:F.63, G:S.64, G:S.64 GLC-GAL-GAL.18: 13 residues within 4Å: Chain H: T.1, T.31, N.32, R.33, T.54, N.55, A.56, G.62, F.63, S.64 Chain I: D.16 Ligands: EMB.25, MEC.26 9 PLIP interactions: 8 interactions with chain H, 1 interactions with chain I Hydrogen bonds: H:F.30, H:N.32, H:N.32, H:R.33, H:R.33, H:F.63, H:S.64, H:S.64, I:D.16 GLC-GAL-GAL.19: 13 residues within 4Å: Chain I: T.1, T.31, N.32, R.33, T.54, N.55, A.56, G.62, F.63, S.64 Chain J: D.16 Ligands: EMB.27, MEC.28 9 PLIP interactions: 8 interactions with chain I, 1 interactions with chain J Hydrogen bonds: I:F.30, I:N.32, I:N.32, I:R.33, I:R.33, I:F.63, I:S.64, I:S.64, J:D.16 GLC-GAL-GAL.20: 13 residues within 4Å: Chain F: D.16 Chain J: T.1, T.31, N.32, R.33, T.54, N.55, A.56, G.62, F.63, S.64 Ligands: EMB.29, MEC.30 8 PLIP interactions: 8 interactions with chain J Hydrogen bonds: J:T.31, J:N.32, J:N.32, J:R.33, J:R.33, J:F.63, J:S.64, J:S.64

10 x EMB: METHYL-CARBAMIC ACID ETHYL ESTER(Non-covalent)(Non-functional Binders)

EMB.6: 5 residues within 4Å: Chain A: N.32 Ligands: GLC-GAL-GAL.1, GLC-GAL-GAL.1, GLC-GAL-GAL.1, MEC.7 No protein-ligand interaction detected (PLIP) EMB.8: 5 residues within 4Å: Chain B: N.32 Ligands: GLC-GAL-GAL.2, GLC-GAL-GAL.2, GLC-GAL-GAL.2, MEC.9 No protein-ligand interaction detected (PLIP) EMB.10: 4 residues within 4Å: Chain C: N.32 Ligands: GLC-GAL-GAL.3, GLC-GAL-GAL.3, MEC.11 No protein-ligand interaction detected (PLIP) EMB.12: 3 residues within 4Å: Ligands: GLC-GAL-GAL.4, GLC-GAL-GAL.4, MEC.13 No protein-ligand interaction detected (PLIP) EMB.14: 3 residues within 4Å: Ligands: GLC-GAL-GAL.5, GLC-GAL-GAL.5, MEC.15 No protein-ligand interaction detected (PLIP) EMB.21: 5 residues within 4Å: Chain F: N.32 Ligands: GLC-GAL-GAL.16, GLC-GAL-GAL.16, GLC-GAL-GAL.16, MEC.22 No protein-ligand interaction detected (PLIP) EMB.23: 5 residues within 4Å: Chain G: N.32 Ligands: GLC-GAL-GAL.17, GLC-GAL-GAL.17, GLC-GAL-GAL.17, MEC.24 No protein-ligand interaction detected (PLIP) EMB.25: 4 residues within 4Å: Chain H: N.32 Ligands: GLC-GAL-GAL.18, GLC-GAL-GAL.18, MEC.26 No protein-ligand interaction detected (PLIP) EMB.27: 3 residues within 4Å: Ligands: GLC-GAL-GAL.19, GLC-GAL-GAL.19, MEC.28 No protein-ligand interaction detected (PLIP) EMB.29: 3 residues within 4Å: Ligands: GLC-GAL-GAL.20, GLC-GAL-GAL.20, MEC.30 No protein-ligand interaction detected (PLIP)

10 x MEC: ETHYL-CARBAMIC ACID METHYL ESTER(Non-covalent)

MEC.7: 4 residues within 4Å: Chain A: N.32, R.33 Ligands: GLC-GAL-GAL.1, EMB.6 No protein-ligand interaction detected (PLIP) MEC.9: 4 residues within 4Å: Chain B: N.32, R.33 Ligands: GLC-GAL-GAL.2, EMB.8 No protein-ligand interaction detected (PLIP) MEC.11: 4 residues within 4Å: Chain C: N.32, R.33 Ligands: GLC-GAL-GAL.3, EMB.10 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.32 MEC.13: 4 residues within 4Å: Chain D: N.32, R.33 Ligands: GLC-GAL-GAL.4, EMB.12 No protein-ligand interaction detected (PLIP) MEC.15: 4 residues within 4Å: Chain E: N.32, R.33 Ligands: GLC-GAL-GAL.5, EMB.14 No protein-ligand interaction detected (PLIP) MEC.22: 4 residues within 4Å: Chain F: N.32, R.33 Ligands: GLC-GAL-GAL.16, EMB.21 No protein-ligand interaction detected (PLIP) MEC.24: 4 residues within 4Å: Chain G: N.32, R.33 Ligands: GLC-GAL-GAL.17, EMB.23 No protein-ligand interaction detected (PLIP) MEC.26: 4 residues within 4Å: Chain H: N.32, R.33 Ligands: GLC-GAL-GAL.18, EMB.25 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:N.32 MEC.28: 4 residues within 4Å: Chain I: N.32, R.33 Ligands: GLC-GAL-GAL.19, EMB.27 No protein-ligand interaction detected (PLIP) MEC.30: 4 residues within 4Å: Chain J: N.32, R.33 Ligands: GLC-GAL-GAL.20, EMB.29 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kitov, P.I. et al., Shiga-like toxins are neutralized by tailored multivalent carbohydrate ligands. Nature (2000)

Release Date

2000-04-11

Peptides

Shiga toxin 1 variant B subunit: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
A

G
B

H
C

I
D

J
E

Shiga toxin 1 variant B subunit

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