SMTL ID : 2c5c.1 (1 other biounit)

Shiga-like toxin 1 B subunit complexed with a bivalent inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.94 Å

Oligo State

homo-pentamer

Ligands

7 x GLC- GAL- GLA: alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose(Non-covalent)(Non-functional Binders)

GLC-GAL-GLA.1: 8 residues within 4Å: Chain A: N.32, R.33, W.34, N.35 Chain B: Y.14, D.18, W.34 Ligands: S10.13 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:W.34, A:N.35, B:Y.14, B:Y.14 GLC-GAL-GLA.2: 12 residues within 4Å: Chain A: T.1, F.30, T.31, N.32, R.33, T.54, N.55, A.56, G.62, F.63, S.64 Chain B: D.16 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.55, A:G.62, A:F.30, A:N.32, A:N.32, A:R.33, A:R.33, A:F.63, B:D.16, A:N.55 GLC-GAL-GLA.3: 8 residues within 4Å: Chain B: N.32, R.33, W.34, N.35 Chain C: Y.14, D.18, W.34 Ligands: S10.13 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 GLC-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:G.62, B:T.31, B:N.32, B:N.32, B:R.33, B:R.33, B:F.63, B:S.64, B:S.64 GLC-GAL-GLA.5: 4 residues within 4Å: Chain B: N.15, D.17, T.19, F.30 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.19, B:T.19 Water bridges: B:K.13 GLC-GAL-GLA.7: 1 residues within 4Å: Ligands: S10.15 No protein-ligand interaction detected (PLIP) GLC-GAL-GLA.12: 12 residues within 4Å: Chain A: D.16 Chain E: T.1, F.30, T.31, N.32, R.33, T.54, N.55, G.62, F.63, S.64 Ligands: S10.17 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:N.55, E:F.30, E:N.32, E:N.32, E:R.33, E:F.63, A:D.16, E:N.55

3 x GLA- GLA: alpha-D-galactopyranose-(1-4)-alpha-D-galactopyranose(Non-covalent)

GLA-GLA.6: 11 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 Ligands: S10.15 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:T.31, C:N.32, C:R.33, C:R.33, C:F.63, C:S.64, D:D.16, D:D.16 GLA-GLA.8: 8 residues within 4Å: Chain D: N.32, R.33, W.34, N.35 Chain E: Y.14, D.18, W.34 Ligands: S10.13 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.32, D:R.33, D:W.34, D:N.35 GLA-GLA.11: 7 residues within 4Å: Chain A: Y.14, D.18 Chain E: N.32, R.33, W.34, N.35 Ligands: S10.13 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain E Hydrogen bonds: A:Y.14, A:D.18, E:W.34, E:N.35, E:N.35

2 x BGC- GAL- GLA: alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose(Non-covalent)(Non-functional Binders)

BGC-GAL-GLA.9: 11 residues within 4Å: Chain D: T.1, T.31, N.32, R.33, T.54, N.55, G.62, F.63, S.64 Chain E: D.16 Ligands: S10.16 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.55, D:G.62, D:T.31, D:T.31, D:N.32, D:N.32, D:R.33, D:R.33, D:F.63, D:S.64, D:S.64, D:N.55 BGC-GAL-GLA.10: 2 residues within 4Å: Chain D: H.58 Ligands: S10.16 No protein-ligand interaction detected (PLIP)

4 x S10: DIETHYL PROPANE-1,3-DIYLBISCARBAMATE(Non-covalent)(Non-functional Binders)

S10.13: 7 residues within 4Å: Chain B: W.34 Ligands: GLC-GAL-GLA.1, GLC-GAL-GLA.1, GLC-GAL-GLA.3, GLC-GAL-GLA.3, GLA-GLA.8, GLA-GLA.11 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.34 S10.15: 3 residues within 4Å: Ligands: GLA-GLA.6, GLC-GAL-GLA.7, GLC-GAL-GLA.7 No protein-ligand interaction detected (PLIP) S10.16: 8 residues within 4Å: Chain D: F.30, H.58, N.59, G.60 Ligands: BGC-GAL-GLA.9, BGC-GAL-GLA.9, BGC-GAL-GLA.10, BGC-GAL-GLA.10 No protein-ligand interaction detected (PLIP) S10.17: 1 residues within 4Å: Ligands: GLC-GAL-GLA.12 No protein-ligand interaction detected (PLIP)

1 x GLA: alpha-D-galactopyranose(Non-covalent)

GLA.14: 6 residues within 4Å: Chain C: N.32, R.33, W.34, N.35 Chain D: Y.14, W.34 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:W.34, C:N.35, C:N.35

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Dodd, R.B. et al., Extensive Cross-Linking of the Shiga-Like Toxin 1 B Subunit by a Bivalent Ligand. To be Published

Release Date

2006-11-27

Peptides

SHIGA-LIKE TOXIN 1 B SUBUNIT: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

SHIGA-LIKE TOXIN 1 B SUBUNIT

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