SMTL ID : 4ks6.1

Crystal structure of the catalytic domain of botulinum neurotoxin BoNT/A C134S mutant with covalent inhibitor that modifies Cys-165 causing disorder in 166-174 stretch

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

monomer

Ligands

1 x MPT- DPP- DAR- GLY- DPN- NH2: Peptide inhibitor MPT-DPP-DAR-G-DPN-NH2(Non-covalent)

MPT-DPP-DAR-GLY-DPN-NH2.1: 19 residues within 4Å: Chain A: Q.182, F.183, E.184, C.185, F.214, T.235, H.243, E.244, H.247, Y.271, L.276, E.282, R.383, Y.386, N.388, F.389, D.390, F.443 Ligands: ZN.2 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:F.183, A:Y.271, A:L.276 Hydrogen bonds: A:F.183, A:T.235, A:E.244, A:E.282, A:R.383, A:R.383, A:Y.386, A:N.388, A:D.390 Water bridges: A:C.185, A:E.244, A:E.282, A:N.388, A:N.388, A:D.390, A:D.390, A:D.390 Salt bridges: A:D.390

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.243, E.244, H.247, E.282 Ligands: MPT-DPP-DAR-GLY-DPN-NH2.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.243, A:H.247, A:E.282, A:E.282

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

SO4.3: 6 residues within 4Å: Chain A: K.395, I.396, N.397, N.432, F.433, T.434 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.434, A:T.434 Water bridges: A:N.403

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: N.420, N.422, I.428 Ligands: EDO.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.422 Water bridges: A:N.425 GOL.5: 2 residues within 4Å: Chain A: K.435, L.436 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.436 Water bridges: A:N.438, A:N.438 GOL.8: 3 residues within 4Å: Chain A: N.403, M.431, N.432 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.403, A:M.431

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 5 residues within 4Å: Chain A: K.26, Q.27, F.28, K.109, T.112 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.28, A:T.112

2 x PGO: S-1,2-PROPANEDIOL(Non-covalent)

PGO.7: 6 residues within 4Å: Chain A: R.303, L.304, Y.307, K.355, F.358, D.359 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.304 Hydrogen bonds: A:R.303, A:R.303, A:D.359 PGO.9: 5 residues within 4Å: Chain A: I.257, N.258, F.302, Y.305, Y.306 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.302 Hydrogen bonds: A:N.258 Water bridges: A:R.261

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

EDO.10: 5 residues within 4Å: Chain A: V.34, Y.41, I.158, Q.159, P.160 1 PLIP interactions: 1 interactions with chain A Water bridges: A:I.158 EDO.11: 4 residues within 4Å: Chain A: I.180, F.208, S.209, F.214 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.209 Water bridges: A:I.180 EDO.12: 5 residues within 4Å: Chain A: K.232, N.425, E.427, I.428 Ligands: GOL.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.232, A:N.425

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guitot, K. et al., Covalent modification of the active site cysteine stresses Clostridium botulinum neurotoxin A. To be Published

Release Date

2014-06-25

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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