SMTL ID : 4elc.1

Crystal structure of the catalytic domain of botulinum neurotoxin BoNT/A C134 mutant with MTSEA modified Cys-165

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.243, H.247, E.282 Ligands: LMR.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.243, A:H.247, A:E.282, A:E.282

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.2: 4 residues within 4Å: Chain A: F.214, R.383, D.390 Ligands: LMR.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.383 pi-Stacking: A:F.214 pi-Cation interactions: A:R.383 IMD.3: 6 residues within 4Å: Chain A: Y.271, R.383, Y.386, N.388, D.390 Ligands: LMR.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.383, A:N.388 Water bridges: A:N.388 pi-Stacking: A:Y.386

1 x LMR: (2S)-2-hydroxybutanedioic acid(Non-covalent)

LMR.4: 11 residues within 4Å: Chain A: F.183, X.185, H.243, E.244, H.247, E.282, R.383, Y.386 Ligands: ZN.1, IMD.2, IMD.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.386 Water bridges: A:F.183 Salt bridges: A:H.243, A:H.247, A:R.383

3 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.5: 6 residues within 4Å: Chain A: S.187, H.190, N.194, L.195, T.196, R.197 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.196, A:R.197 pi-Cation interactions: A:H.190 DMS.10: 6 residues within 4Å: Chain A: K.395, I.396, M.431, N.432, F.433, T.434 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.434 DMS.11: 5 residues within 4Å: Chain A: I.257, N.258, F.302, Y.305, Y.306 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.258 Water bridges: A:N.258, A:R.261

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 1 residues within 4Å: Chain A: K.360 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.360 SO4.7: 3 residues within 4Å: Chain A: N.60, K.61, Y.332 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.60, A:Y.332 Water bridges: A:K.61 Salt bridges: A:K.61

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.8: 3 residues within 4Å: Chain A: A.230, K.435, N.438 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.230 Hydrogen bonds: A:N.438 MPD.9: 3 residues within 4Å: Chain A: A.419, N.420, F.421 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.419, A:F.421 Hydrogen bonds: A:N.420 Water bridges: A:A.418, A:F.421

3 x LI: LITHIUM ION(Non-covalent)

LI.12: 3 residues within 4Å: Chain A: N.430, F.433, T.434 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:N.430, A:F.433, H2O.8, H2O.15 LI.13: 4 residues within 4Å: Chain A: D.94, T.96, Y.97, E.103 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.96, H2O.13, H2O.13, H2O.14 LI.14: 3 residues within 4Å: Chain A: T.405, D.408, R.413 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.405, A:D.408, H2O.8, H2O.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stura, E.A. et al., Structural Framework for Covalent Inhibition of Clostridium botulinum Neurotoxin A by Targeting Cys165. J.Biol.Chem. (2012)

Release Date

2012-08-15

Peptides

Botulinum neurotoxin A light chain: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Botulinum neurotoxin A light chain

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