SMTL ID : 7vhe.1

Crystal structure of the STX2a complexed with RRRA peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-1-5-mer

Ligands

1 x ARG- ARG- ARG- ALA- NH2: RRRA peptide(Non-covalent)

ARG-ARG-ARG-ALA-NH2.1: 14 residues within 4Å: Chain A: Y.77, V.78, D.94, F.95, S.112, S.113, Y.114, L.117, V.162, E.167, R.170, T.199, L.200, W.202 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Y.114, A:Y.114, A:L.117, A:V.162, A:L.200 Hydrogen bonds: A:V.78, A:V.78, A:D.94, A:S.112, A:S.112, A:Y.114, A:T.199 Water bridges: A:N.75, A:Y.77, A:W.202, A:E.259 Salt bridges: A:D.94, A:E.167

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

1PS.2: 5 residues within 4Å: Chain B: 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, B:D.16 Salt bridges: B:K.12 pi-Stacking: B:W.29, B:W.29 1PS.3: 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, C:D.16 pi-Stacking: C:W.29, C:W.29 1PS.4: 5 residues within 4Å: Chain D: N.14, E.15, D.16, T.18, W.29 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:E.15, D:D.16 Water bridges: D:D.16, D:D.16 pi-Stacking: D:W.29, D:W.29 1PS.5: 5 residues within 4Å: Chain F: N.14, E.15, D.16, T.18, W.29 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:E.15, F:D.16 pi-Stacking: F:W.29, F:W.29

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 3 residues within 4Å: Chain A: F.291 Chain F: S.31, W.33 1 PLIP interactions: 1 interactions with chain F Water bridges: F:W.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Watanabe-Takahashi, M. et al., A unique peptide-based pharmacophore identifies an inhibitory compound against the A-subunit of Shiga toxin. Sci Rep (2022)

Release Date

2022-07-20

Peptides

rRNA N-glycosylase: 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

rRNA N-glycosylase

Shiga toxin 2 B subunit

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