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

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.94 Å

Oligo State

homo-pentamer

Ligands

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

GLA-GLA.1: 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: 2 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:Y.14, C:D.18, B:N.32, B:W.34, B:N.35 GLA-GLA.2: 5 residues within 4Å: Chain C: N.32, R.33, W.34, N.35 Chain D: D.18 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:W.34, C:N.35, C:N.35 GLA-GLA.4: 7 residues within 4Å: Chain D: N.32, R.33, W.34, N.35 Chain E: Y.14, D.18, W.34 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:W.34, D:N.35, E:Y.14

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

GLC-GAL-GLA.3: 10 residues within 4Å: Chain C: T.1, N.32, R.33, T.54, N.55, A.56, G.62, F.63, S.64 Chain D: D.16 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:N.32, C:N.32, C:R.33, C:S.64, C:S.64, D:D.16, C:N.55, C:A.56, C:G.62 GLC-GAL-GLA.7: 8 residues within 4Å: Chain A: Y.14, D.18, W.34 Chain E: N.32, R.33, W.34, N.35 Ligands: S10.13 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:R.33, E:W.34, E:N.35, E:N.35 GLC-GAL-GLA.8: 13 residues within 4Å: Chain A: D.16 Chain E: T.1, F.30, T.31, N.32, R.33, T.54, N.55, A.56, G.62, F.63, S.64 Ligands: S10.12 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:T.31, E:N.32, E:N.32, E:R.33, E:R.33, E:F.63, E:S.64, E:S.64, A:D.16, E:N.55 Water bridges: E:E.65

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

BGC-GLA-GLA.5: 13 residues within 4Å: Chain D: T.1, F.30, T.31, N.32, R.33, T.54, N.55, A.56, G.62, F.63, S.64 Chain E: D.16 Ligands: S10.10 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:T.31, D:N.32, D:R.33, D:R.33, D:F.63, E:D.16, D:N.55 BGC-GLA-GLA.6: 1 residues within 4Å: Ligands: S10.10 No protein-ligand interaction detected (PLIP)

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

S10.9: 2 residues within 4Å: Chain B: W.34 Ligands: S10.13 No protein-ligand interaction detected (PLIP) S10.10: 5 residues within 4Å: Ligands: BGC-GLA-GLA.5, BGC-GLA-GLA.5, BGC-GLA-GLA.6, BGC-GLA-GLA.6, SO4.11 No protein-ligand interaction detected (PLIP) S10.12: 6 residues within 4Å: Chain E: D.17, T.19, N.32 Ligands: GLC-GAL-GLA.8, GLC-GAL-GLA.8, GLC-GAL-GLA.8 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.32 S10.13: 3 residues within 4Å: Ligands: GLC-GAL-GLA.7, GLC-GAL-GLA.7, S10.9 No protein-ligand interaction detected (PLIP)

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.11: 2 residues within 4Å: Chain D: H.58 Ligands: S10.10 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:H.58

Links

RCSB   PDBe   PDBe-KB   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
F

B
G

C
H

D
I

E
J

SHIGA-LIKE TOXIN 1 B SUBUNIT

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