SMTL ID : 6x6h.1

Structure of Shiga toxin 2 with a C-terminal peptide of ribosomal P stalk proteins

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

hetero-1-1-5-mer

Ligands

1 x GLY- PHE- GLY- LEU- PHE- ASP: P11 peptide(Non-covalent)

GLY-PHE-GLY-LEU-PHE-ASP.1: 12 residues within 4Å: Chain A: Q.10, Q.11, V.14, N.18, T.36, R.172, Q.175, R.176, R.179, S.229, L.232, G.233 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Q.10, A:V.14, A:V.14, A:T.36, A:L.232, A:L.232 Hydrogen bonds: A:N.18, A:Q.175, A:Q.175, A:R.176 Water bridges: A:T.36, A:T.36, A:R.179, A:R.179 Salt bridges: A:R.172, A:R.179 pi-Cation interactions: A:R.179

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 3 residues within 4Å: Chain A: N.227, I.228, S.229 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain A: S.48, Y.49 Ligand excluded by PLIP CL.4: 1 residues within 4Å: Chain A: V.78 Ligand excluded by PLIP CL.5: 5 residues within 4Å: Chain B: R.9, P.10, E.20, S.21, N.22 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain B: Y.36 Chain E: N.34, L.38 Chain F: Q.36 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain B: K.31, Y.36 Chain E: W.33, N.34 Ligand excluded by PLIP

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 6 residues within 4Å: Chain C: S.31, R.32, W.33, N.34 Chain D: Y.13, D.17 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:W.33, C:N.34, D:Y.13 Water bridges: C:S.31 EDO.8: 6 residues within 4Å: Chain D: S.31, R.32, W.33, N.34 Chain E: Y.13, W.33 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:S.31, D:W.33, D:N.34, E:Y.13, E:Y.13 EDO.11: 8 residues within 4Å: Chain B: K.40 Chain E: S.31, R.32, W.33, N.34 Chain F: Y.13, D.17, W.33 6 PLIP interactions: 2 interactions with chain E, 2 interactions with chain F, 2 interactions with chain B Hydrogen bonds: E:W.33, E:N.34, F:Y.13, F:Y.13, B:K.40, B:K.40 EDO.12: 7 residues within 4Å: Chain B: L.28, R.30 Chain C: P.37, Q.40 Chain G: P.37, L.38, S.41 3 PLIP interactions: 1 interactions with chain G, 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: G:S.41, B:R.30, C:Q.40 EDO.13: 5 residues within 4Å: Chain C: Y.13, W.33 Chain G: R.32, W.33, N.34 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:S.31, G:W.33, G:N.34, G:N.34

2 x ACY: ACETIC ACID(Non-functional Binders)

ACY.7: 6 residues within 4Å: Chain C: W.29, T.30, S.31, R.32, G.61, F.62 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:W.29 Hydrogen bonds: C:T.30, C:S.31, C:R.32 Salt bridges: C:R.32 ACY.14: 6 residues within 4Å: Chain G: W.29, T.30, S.31, R.32, G.61, F.62 6 PLIP interactions: 6 interactions with chain G Hydrophobic interactions: G:W.29 Hydrogen bonds: G:T.30, G:T.30, G:S.31, G:R.32 Salt bridges: G:R.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rudolph, M.J. et al., Structural basis for the interaction of Shiga toxin 2a with a C-terminal peptide of ribosomal P stalk proteins. J.Biol.Chem. (2020)

Release Date

2020-09-09

Peptides

rRNA N-glycosylase: A
rRNA N-glycosylase: B
Shiga toxin 2 B subunit: CDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A1

B
A2

C
B

D
C

E
D

F
E

G
F

rRNA N-glycosylase

rRNA N-glycosylase

Shiga toxin 2 B subunit

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