SMTL ID : 4m1u.1

The crystal structure of Stx2 and a disaccharide ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

hetero-1-5-mer

Ligands

2 x MBG- A2G: 2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-4)-methyl beta-D-galactopyranoside(Non-covalent)

MBG-A2G.1: 8 residues within 4Å: Chain F: K.12, N.14, D.16, T.18, T.20, E.27, W.29, G.59 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:K.12, F:K.12, F:T.20, F:E.27, F:D.16 Water bridges: F:E.15 MBG-A2G.2: 10 residues within 4Å: Chain B: E.15 Chain F: W.29, T.30, S.31, R.32, S.53, S.54, G.61, F.62, A.63 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:W.29, F:T.30, F:S.31, F:R.32, F:R.32, F:F.62, F:S.54, F:G.61, B:E.15

3 x 1PS: 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE(Non-covalent)

1PS.3: 6 residues within 4Å: Chain B: K.12, N.14, E.15, D.16, T.18, W.29 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.15, B:D.16 Water bridges: B:K.12 Salt bridges: B:K.12 pi-Stacking: B:W.29, B:W.29 1PS.4: 5 residues within 4Å: Chain C: N.14, E.15, D.16, T.18, W.29 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.15, C:D.16 Water bridges: C:K.12 pi-Stacking: C:W.29, C:W.29 1PS.5: 5 residues within 4Å: Chain D: N.14, E.15, D.16, T.18, W.29 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:E.15, D:D.16, D:D.16 Water bridges: D:K.12, D:K.12, D:N.14 pi-Stacking: D:W.29, D:W.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jacobson, J.M. et al., The crystal structure of shiga toxin type 2 with bound disaccharide guides the design of a heterobifunctional toxin inhibitor. J.Biol.Chem. (2014)

Release Date

2013-11-20

Peptides

Shiga toxin 2 A-subunit: A
Shiga toxin 2 B subunit: BCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Shiga toxin 2 A-subunit

Shiga toxin 2 B subunit

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