SMTL ID : 7mjr.1

Vip4Da2 toxin structure

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.22 Å

Oligo State

monomer

Ligands

3 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.187, D.189, D.191, I.193, E.198 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.187, A:D.189, A:D.191, A:I.193, A:E.198 CA.2: 7 residues within 4Å: Chain A: D.189, D.191, E.198, N.227, H.230, A.231, D.240 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.191, A:E.198, A:N.227, A:H.230, A:D.240 CA.3: 6 residues within 4Å: Chain A: F.599, E.600, T.617, G.618, K.620, D.718 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.617, A:D.718

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

SO4.4: 2 residues within 4Å: Chain A: R.354, K.429 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.354, A:K.429 SO4.5: 3 residues within 4Å: Chain A: W.329, Q.453, R.477 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.477 SO4.6: 4 residues within 4Å: Chain A: H.230, K.235, N.506, R.584 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.506 Salt bridges: A:H.230, A:K.235, A:R.584 SO4.7: 4 residues within 4Å: Chain A: R.567, Q.568, K.581, K.583 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.567, A:K.581, A:K.583 SO4.8: 3 residues within 4Å: Chain A: I.624, G.625, G.628 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.625 SO4.9: 3 residues within 4Å: Chain A: N.697, N.698, Q.732 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.697, A:Q.732 SO4.10: 3 residues within 4Å: Chain A: H.735, I.736, F.737 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.737 SO4.11: 4 residues within 4Å: Chain A: R.771, G.773, S.774, Y.791 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.774, A:Y.791 Salt bridges: A:R.771 SO4.12: 3 residues within 4Å: Chain A: G.820, E.821, S.822 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.822, A:E.823

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kouadio, J.L. et al., Structural and functional insights into the first Bacillus thuringiensis vegetative insecticidal protein of the Vpb4 fold, active against western corn rootworm. Plos One (2021)

Release Date

2021-05-05

Peptides

Vip4Da1 protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Vip4Da1 protein