SMTL ID : 2ga4.1

Stx2 with adenine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-5-mer

Ligands

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

NA.1: 5 residues within 4Å: Chain A: R.266, P.267, S.278, N.279 Ligands: FMT.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.266, A:N.279, A:N.279 Water bridges: A:N.207 NA.2: 2 residues within 4Å: Chain A: T.22, S.25 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.25 NA.3: 3 residues within 4Å: Chain A: S.15, S.16, S.19 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.15, A:S.19 NA.7: 4 residues within 4Å: Chain B: S.53, T.55, S.60, G.61 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.53, B:S.53 NA.14: 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

1 x ADE: ADENINE(Non-covalent)

ADE.4: 9 residues within 4Å: Chain A: L.76, Y.77, V.78, S.112, Y.114, V.162, A.166, E.167, R.170 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:V.78, A:S.112, A:E.167, A:R.170, A:R.170 Water bridges: A:Y.114 pi-Stacking: A:Y.77, A:Y.77

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

FMT.5: 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.6: 8 residues within 4Å: Chain A: N.207, Q.261, T.263, D.265, R.266, P.267, N.279 Ligands: NA.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.207, A:R.266 Water bridges: A:N.207, A:C.260, A:N.279, A:N.279 FMT.10: 3 residues within 4Å: Chain C: S.31, R.32, W.33 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain C Water bridges: D:D.17, C:R.32, C:N.34, C:N.34 Hydrogen bonds: C:W.33 FMT.12: 4 residues within 4Å: Chain D: T.20, W.29, G.59 Ligands: 1PS.11 No protein-ligand interaction detected (PLIP) FMT.13: 6 residues within 4Å: Chain A: T.294 Chain E: R.32, W.33, N.34 Chain F: Y.13, D.17 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:N.34, F:Y.13, F:Y.13 Water bridges: E:W.33, E:W.33

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

1PS.8: 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, B:D.16 Salt bridges: B:K.12 pi-Stacking: B:W.29, B:W.29 1PS.9: 5 residues within 4Å: Chain C: N.14, E.15, D.16, T.18, W.29 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:E.15, C:D.16, C:D.16 Water bridges: C:K.12 pi-Stacking: C:W.29, C:W.29 1PS.11: 7 residues within 4Å: Chain D: K.12, N.14, E.15, D.16, T.18, W.29 Ligands: FMT.12 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:E.15, D:D.16, D:D.16 Water bridges: D:K.12, D:K.12, D:E.15, D:E.15 Salt bridges: D:K.12 pi-Stacking: D:W.29, D:W.29 1PS.15: 6 residues within 4Å: Chain F: K.12, 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 Salt bridges: F:K.12 pi-Stacking: F:W.29, F:W.29

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

EDO.16: 7 residues within 4Å: Chain A: F.291 Chain B: Y.13, D.17 Chain F: S.31, R.32, W.33, N.34 5 PLIP interactions: 2 interactions with chain F, 3 interactions with chain B Hydrogen bonds: F:W.33, F:N.34, B:Y.13, B:Y.13, B:D.17

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fraser, M.E. et al., Binding of adenine to Stx2, the protein toxin from Escherichia coli O157:H7. Acta Crystallogr.,Sect.F (2006)

Release Date

2006-07-11

Peptides

Shiga-like toxin II subunit A: A
Shiga-like toxin II subunit B: BCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Shiga-like toxin II subunit A

Shiga-like toxin II subunit B

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