SMTL ID : 7ujj.1

Stx2a and DARPin complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-5-mer

Ligands

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

1PS.1: 16 residues within 4Å: Chain A: A.74, D.75, G.76, L.105, L.108, D.109, G.110, H.111, R.142, H.144 Chain C: K.12, N.14, E.15, D.16, T.18, W.29 13 PLIP interactions: 4 interactions with chain C, 9 interactions with chain A Hydrogen bonds: C:D.16, A:D.109, A:D.109 Salt bridges: C:K.12, A:R.142, A:H.144 pi-Stacking: C:W.29, C:W.29 Hydrophobic interactions: A:D.75, A:L.105, A:D.109 Water bridges: A:G.110, A:G.110 1PS.16: 8 residues within 4Å: Chain A: S.31, N.32 Chain D: N.14, E.15, D.16, T.18, W.29 Ligands: FMT.18 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 Salt bridges: D:K.12 pi-Stacking: D:W.29, D:W.29 1PS.19: 7 residues within 4Å: Chain E: K.12, N.14, E.15, D.16, T.18, W.29 Ligands: FMT.21 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:N.14, E:E.15, E:D.16, E:D.16 Water bridges: E:K.12 Salt bridges: E:K.12 pi-Stacking: E:W.29, E:W.29 1PS.26: 5 residues within 4Å: Chain G: N.14, E.15, D.16, T.18, W.29 6 PLIP interactions: 6 interactions with chain G Hydrogen bonds: G:E.15, G:D.16, G:D.16 Water bridges: G:D.16 pi-Stacking: G:W.29, G:W.29

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

FMT.2: 7 residues within 4Å: Chain A: R.141, I.171, D.174, N.175 Chain G: S.31, R.32 Ligands: EDO.28 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.175 FMT.8: 4 residues within 4Å: Chain B: V.14, Q.175, R.176, R.179 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.175, B:R.179 Water bridges: B:R.176 FMT.9: 8 residues within 4Å: Chain B: N.207, Q.261, T.263, G.264, D.265, R.266, P.267 Ligands: NA.4 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.207, B:R.266, B:N.279 Water bridges: B:N.279 FMT.10: 3 residues within 4Å: Chain B: R.266, V.268, I.269 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.266 FMT.11: 4 residues within 4Å: Chain B: T.110, V.120, T.149, M.150 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:M.150 Water bridges: B:D.111 FMT.12: 4 residues within 4Å: Chain B: Q.129, I.130, S.131, S.134 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.129, B:S.131, B:S.134 FMT.13: 5 residues within 4Å: Chain B: Y.77, V.78, S.112, Y.114, V.162 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.78, B:V.78 FMT.15: 5 residues within 4Å: Chain C: N.68, N.69 Chain D: I.8, E.9, Q.43 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:N.69, C:N.69, D:Q.43 Water bridges: C:N.68, C:D.70 FMT.17: 3 residues within 4Å: Chain D: S.31, R.32, W.33 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:W.33 Water bridges: D:N.34, D:N.34 FMT.18: 4 residues within 4Å: Chain D: T.20, W.29, G.59 Ligands: 1PS.16 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.59 Water bridges: D:K.12 FMT.21: 4 residues within 4Å: Chain E: T.20, W.29, G.59 Ligands: 1PS.19 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:T.20, E:T.20 FMT.22: 6 residues within 4Å: Chain B: T.294 Chain F: R.32, W.33, N.34 Chain G: Y.13, D.17 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:N.34 Water bridges: F:W.33, F:W.33 FMT.23: 5 residues within 4Å: Chain F: W.29, T.30, S.31, R.32, F.62 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:T.30, F:S.31, F:R.32, F:R.32 FMT.24: 8 residues within 4Å: Chain B: R.219, R.222, S.224 Chain F: T.45, G.46, M.47, N.69, D.70 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.224, B:S.224 Water bridges: B:R.219 FMT.29: 5 residues within 4Å: Chain F: N.68, N.69 Chain G: I.8, E.9, Q.43 6 PLIP interactions: 5 interactions with chain F, 1 interactions with chain G Hydrogen bonds: F:N.69, F:N.69, G:Q.43 Water bridges: F:N.68, F:D.70, F:D.70

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

NA.3: 2 residues within 4Å: Chain B: T.22, S.25 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.22 NA.4: 5 residues within 4Å: Chain B: R.266, P.267, S.278, N.279 Ligands: FMT.9 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.207, B:N.279, B:N.279 NA.5: 2 residues within 4Å: Chain B: S.15, S.19 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.19, B:S.19 NA.14: 8 residues within 4Å: Chain A: R.34, L.39, V.42, L.72 Chain C: S.53, T.55, S.60, G.61 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:T.55, A:R.34, A:R.34, A:R.34 NA.25: 6 residues within 4Å: Chain A: G.176, N.177 Chain G: S.53, T.55, S.60, G.61 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain A Hydrogen bonds: G:S.53, G:T.55, A:G.176

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

EDO.6: 4 residues within 4Å: Chain B: K.288, L.292 Chain D: W.33, N.34 No protein-ligand interaction detected (PLIP) EDO.7: 5 residues within 4Å: Chain B: F.3, T.4, S.16, S.19, I.20 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.4, B:S.16 EDO.20: 5 residues within 4Å: Chain B: K.288, L.292, G.296 Chain D: N.34 Chain E: W.33 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:K.288, D:N.34 Water bridges: B:G.296 EDO.27: 8 residues within 4Å: Chain B: F.291 Chain C: Y.13, D.17 Chain G: S.31, R.32, W.33, N.34 Ligands: EDO.28 4 PLIP interactions: 2 interactions with chain G, 2 interactions with chain C Hydrogen bonds: G:W.33, G:N.34, C:Y.13, C:Y.13 EDO.28: 4 residues within 4Å: Chain G: S.31, W.33 Ligands: FMT.2, EDO.27 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:S.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zeng, Y. et al., A Multi-Specific DARPin Potently Neutralizes Shiga Toxin 2 via Simultaneous Modulation of Both Toxin Subunits. Bioengineering (Basel) (2022)

Release Date

2023-04-12

Peptides

DARPin: A
Shiga-like toxin 2 subunit A: B
Shiga-like toxin 2 subunit B: CDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
A

C
B

D
C

E
D

F
E

G
F

DARPin

Shiga-like toxin 2 subunit A

Shiga-like toxin 2 subunit B

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