SMTL ID : 1r4p.1

Shiga toxin type 2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

hetero-oligomer

Ligands

5 x NA: SODIUM ION(Non-functional Binders)

NA.1: 2 residues within 4Å: Chain A: T.22, S.25 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.25 NA.2: 5 residues within 4Å: Chain A: R.266, P.267, S.278, N.279 Ligands: FMT.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.207, A:P.267, A:N.279 NA.3: 2 residues within 4Å: Chain A: S.15, S.19 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.15, A:S.19 NA.12: 4 residues within 4Å: Chain B: S.53, T.55, S.60, G.61 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.53, B:T.55, B:G.61 NA.24: 4 residues within 4Å: Chain F: S.53, T.55, S.60, G.61 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:S.53, F:T.55, F:T.55

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

EDO.4: 4 residues within 4Å: Chain A: K.288, L.292 Chain C: W.33, N.34 No protein-ligand interaction detected (PLIP) EDO.5: 5 residues within 4Å: Chain A: F.3, T.4, S.16, S.19, I.20 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.4, A:S.16 EDO.19: 5 residues within 4Å: Chain A: K.288, L.292, G.296 Chain C: N.34 Chain D: W.33 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:K.288, C:N.34 Water bridges: A:G.296 EDO.26: 8 residues within 4Å: Chain A: F.291 Chain B: Y.13, D.17 Chain F: S.31, R.32, W.33, N.34 Ligands: EDO.27 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain B Hydrogen bonds: F:W.33, F:N.34, B:Y.13, B:Y.13 EDO.27: 4 residues within 4Å: Chain F: S.31, W.33 Ligands: EDO.26, FMT.28 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:S.31

15 x FMT: FORMIC ACID(Non-functional Binders)

FMT.6: 4 residues within 4Å: Chain A: V.14, Q.175, R.176, R.179 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.175, A:R.179 Water bridges: A:R.176 FMT.7: 8 residues within 4Å: Chain A: N.207, Q.261, T.263, G.264, D.265, R.266, P.267 Ligands: NA.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.207, A:R.266, A:N.279 Water bridges: A:N.279 FMT.8: 3 residues within 4Å: Chain A: R.266, V.268, I.269 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.266 FMT.9: 4 residues within 4Å: Chain A: T.110, V.120, T.149, M.150 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.109, A:M.150 Water bridges: A:D.111 FMT.10: 4 residues within 4Å: Chain A: Q.129, I.130, S.131, S.134 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.129, A:S.131, A:S.134 FMT.11: 5 residues within 4Å: Chain A: Y.77, V.78, S.112, Y.114, V.162 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.78, A:V.78 FMT.14: 5 residues within 4Å: Chain B: N.68, N.69 Chain C: I.8, E.9, Q.43 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:N.69, B:N.69, C:Q.43 Water bridges: B:N.68, B:D.70 FMT.16: 3 residues within 4Å: Chain C: S.31, R.32, W.33 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:W.33 Water bridges: C:N.34 FMT.17: 4 residues within 4Å: Chain C: T.20, W.29, G.59 Ligands: 1PS.15 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.20, C:G.59 Water bridges: C:K.12 FMT.20: 4 residues within 4Å: Chain D: T.20, W.29, G.59 Ligands: 1PS.18 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.20 FMT.21: 6 residues within 4Å: Chain A: T.294 Chain E: R.32, W.33, N.34 Chain F: Y.13, D.17 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:N.34, F:Y.13 Water bridges: E:W.33, E:W.33 FMT.22: 5 residues within 4Å: Chain E: W.29, T.30, S.31, R.32, F.62 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:S.31, E:R.32, E:R.32 FMT.23: 8 residues within 4Å: Chain A: R.219, R.222, S.224 Chain E: T.45, G.46, M.47, N.69, D.70 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:N.69, A:S.224 Water bridges: A:R.219 FMT.28: 3 residues within 4Å: Chain F: S.31, R.32 Ligands: EDO.27 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:S.31 FMT.29: 5 residues within 4Å: Chain E: N.68, N.69 Chain F: I.8, E.9, Q.43 6 PLIP interactions: 1 interactions with chain F, 5 interactions with chain E Hydrogen bonds: F:Q.43, E:N.69, E:N.69 Water bridges: E:N.68, E:D.70, E:D.70

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

1PS.13: 6 residues within 4Å: Chain B: K.12, N.14, E.15, D.16, T.18, W.29 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.14, B:E.15, B:D.16, B:D.16 Salt bridges: B:K.12 pi-Stacking: B:W.29, B:W.29 1PS.15: 6 residues within 4Å: Chain C: N.14, E.15, D.16, T.18, W.29 Ligands: FMT.17 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:N.14, C:E.15, C:D.16, C:D.16 Water bridges: C:T.20 Salt bridges: C:K.12 pi-Stacking: C:W.29, C:W.29 1PS.18: 7 residues within 4Å: Chain D: K.12, N.14, E.15, D.16, T.18, W.29 Ligands: FMT.20 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:N.14, D:E.15, D:D.16, D:D.16 Water bridges: D:K.12 Salt bridges: D:K.12 pi-Stacking: D:W.29, D:W.29 1PS.25: 5 residues within 4Å: Chain F: N.14, E.15, D.16, T.18, W.29 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:N.14, F:E.15, F:D.16, F:D.16 pi-Stacking: F:W.29, F:W.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fraser, M.E. et al., Structure of Shiga Toxin Type 2 (Stx2) from Escherichia coli O157:H7. J.Biol.Chem. (2004)

Release Date

2004-05-11

Peptides

shiga-like toxin type II A subunit: A
shiga-like toxin type II B subunit: BCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

shiga-like toxin type II A subunit

shiga-like toxin type II B subunit

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