SMTL ID : 2yeo.1

A39L mutation of scorpion toxin lqh-alpha-it

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.08 Å

Oligo State

homo-trimer

Ligands

3 x DR8: N,N,N-TRIMETHYLHEPTA-1,3,5-TRIYN-1-AMINIUM(Non-covalent)

DR8.1: 17 residues within 4Å: Chain A: Y.36, Y.50 Chain B: Y.36, Y.50 Chain C: Y.36, Y.50 Ligands: DR0.2, EDO.3, CL.6, DR8.10, DR0.11, EDO.12, CL.15, DR8.19, DR0.20, EDO.21, CL.24 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C pi-Cation interactions: A:Y.36, B:Y.36, C:Y.36 DR8.10: 17 residues within 4Å: Chain A: Y.36, Y.50 Chain B: Y.36, Y.50 Chain C: Y.36, Y.50 Ligands: DR8.1, DR0.2, EDO.3, CL.6, DR0.11, EDO.12, CL.15, DR8.19, DR0.20, EDO.21, CL.24 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C pi-Cation interactions: A:Y.36, B:Y.36, C:Y.36 DR8.19: 17 residues within 4Å: Chain A: Y.36, Y.50 Chain B: Y.36, Y.50 Chain C: Y.36, Y.50 Ligands: DR8.1, DR0.2, EDO.3, CL.6, DR8.10, DR0.11, EDO.12, CL.15, DR0.20, EDO.21, CL.24 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C pi-Cation interactions: A:Y.36, B:Y.36, C:Y.36

3 x DR0: N-(HYDROXYMETHYL)-N,N-DIMETHYLHEXAN-1-AMINIUM(Non-covalent)

DR0.2: 16 residues within 4Å: Chain A: W.39, L.40 Chain B: F.18, D.20, Y.36, C.37, Q.38, W.39 Ligands: DR8.1, CL.6, DR8.10, DR0.11, CL.15, EDO.18, DR8.19, DR0.20 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Water bridges: B:D.20, B:D.20 Salt bridges: B:D.20 pi-Cation interactions: B:W.39, B:W.39 Hydrophobic interactions: A:W.39 DR0.11: 16 residues within 4Å: Chain B: W.39, L.40 Chain C: F.18, D.20, Y.36, C.37, Q.38, W.39 Ligands: DR8.1, DR0.2, DR8.10, CL.15, DR8.19, DR0.20, CL.24, EDO.27 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B Water bridges: C:D.20, C:D.20 Salt bridges: C:D.20 pi-Cation interactions: C:W.39, C:W.39 Hydrophobic interactions: B:W.39 DR0.20: 16 residues within 4Å: Chain A: F.18, D.20, Y.36, C.37, Q.38, W.39 Chain C: W.39, L.40 Ligands: DR8.1, DR0.2, CL.6, EDO.9, DR8.10, DR0.11, DR8.19, CL.24 6 PLIP interactions: 1 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: C:W.39 Water bridges: A:D.20, A:D.20 Salt bridges: A:D.20 pi-Cation interactions: A:W.39, A:W.39

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

EDO.3: 15 residues within 4Å: Chain A: Y.6, Y.36, Q.38, W.48, Y.50 Chain B: D.20, A.21, N.24, S.34, G.35, Y.36 Ligands: DR8.1, EDO.4, DR8.10, DR8.19 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:D.20, A:Y.36, A:Q.38, A:Y.50 Water bridges: A:W.48 EDO.4: 9 residues within 4Å: Chain A: Y.6, Q.38, K.42, W.48 Chain B: D.20, A.21, N.24, E.25 Ligands: EDO.3 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.24, A:Y.6, A:Q.38 Water bridges: B:A.21 EDO.7: 7 residues within 4Å: Chain A: I.7, A.8, K.9, Y.15, N.30, V.56, P.57 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.15, A:N.30 EDO.9: 6 residues within 4Å: Chain A: F.18, R.19, D.20, W.39 Chain C: L.40 Ligands: DR0.20 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:F.18, C:L.40 Water bridges: A:D.20 EDO.12: 15 residues within 4Å: Chain B: Y.6, Y.36, Q.38, W.48, Y.50 Chain C: D.20, A.21, N.24, S.34, G.35, Y.36 Ligands: DR8.1, DR8.10, EDO.13, DR8.19 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Y.36, B:Q.38, B:Y.50, C:D.20 Water bridges: B:W.48 EDO.13: 9 residues within 4Å: Chain B: Y.6, Q.38, K.42, W.48 Chain C: D.20, A.21, N.24, E.25 Ligands: EDO.12 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:Y.6, B:Q.38, C:N.24 Water bridges: C:A.21 EDO.16: 7 residues within 4Å: Chain B: I.7, A.8, K.9, Y.15, N.30, V.56, P.57 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.15, B:N.30 EDO.18: 6 residues within 4Å: Chain A: L.40 Chain B: F.18, R.19, D.20, W.39 Ligands: DR0.2 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:L.40, B:F.18 Water bridges: B:D.20 EDO.21: 15 residues within 4Å: Chain A: D.20, A.21, N.24, S.34, G.35, Y.36 Chain C: Y.6, Y.36, Q.38, W.48, Y.50 Ligands: DR8.1, DR8.10, DR8.19, EDO.22 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Y.36, C:Q.38, C:Y.50, A:D.20 Water bridges: C:W.48 EDO.22: 9 residues within 4Å: Chain A: D.20, A.21, N.24, E.25 Chain C: Y.6, Q.38, K.42, W.48 Ligands: EDO.21 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:Y.6, C:Q.38, A:N.24 Water bridges: A:A.21 EDO.25: 7 residues within 4Å: Chain C: I.7, A.8, K.9, Y.15, N.30, V.56, P.57 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.15, C:N.30 EDO.27: 6 residues within 4Å: Chain B: L.40 Chain C: F.18, R.19, D.20, W.39 Ligands: DR0.11 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:F.18, B:L.40 Water bridges: C:D.20

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

CL.5: 4 residues within 4Å: Chain A: C.13, V.14, R.59, C.64 Ligand excluded by PLIP CL.6: 8 residues within 4Å: Chain A: Y.36, Q.38, W.39 Ligands: DR8.1, DR0.2, DR8.10, DR8.19, DR0.20 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: R.19, A.21 Chain C: K.42 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain B: C.13, V.14, R.59, C.64 Ligand excluded by PLIP CL.15: 8 residues within 4Å: Chain B: Y.36, Q.38, W.39 Ligands: DR8.1, DR0.2, DR8.10, DR0.11, DR8.19 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain A: K.42 Chain B: R.19, A.21 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain C: C.13, V.14, R.59, C.64 Ligand excluded by PLIP CL.24: 8 residues within 4Å: Chain C: Y.36, Q.38, W.39 Ligands: DR8.1, DR8.10, DR0.11, DR8.19, DR0.20 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain B: K.42 Chain C: R.19, A.21 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Frolow, F. et al., Crystal Structures of Scorpion Alpha-Toxinsmutants Reveal Conformational Constraints that Dictate Preference for Mammalian Brain Voltage-Gated Na- Channels. To be Published

Release Date

2011-04-13

Peptides

ALPHA-INSECT TOXIN LQHAIT: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

ALPHA-INSECT TOXIN LQHAIT