SMTL ID : 6w08.1

Crystal Structure of Motility Associated Killing Factor E from Vibrio cholerae

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

1 x ACY: ACETIC ACID(Non-functional Binders)

ACY.1: 5 residues within 4Å: Chain A: W.61, N.66, Y.131, G.134, L.135 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.66 Water bridges: A:S.64, A:S.64

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

EDO.2: 6 residues within 4Å: Chain A: I.35, D.36 Chain B: K.56, R.59, Q.60 Ligands: EDO.4 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.59 EDO.3: 8 residues within 4Å: Chain A: F.184, F.200, E.201, T.202, S.225, S.226, A.230, I.234 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.202, A:T.202, A:S.226, A:A.230 Water bridges: A:T.348 EDO.4: 8 residues within 4Å: Chain A: T.33, Y.34, I.35, L.51, N.52, Q.55 Chain B: R.59 Ligands: EDO.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.35, A:I.35, A:N.52 EDO.6: 6 residues within 4Å: Chain B: G.65, N.66, L.67, F.69, S.70, N.71 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.66, B:L.67, B:N.71 Water bridges: B:F.69, B:F.69, B:S.70 EDO.9: 5 residues within 4Å: Chain B: V.207, P.210, N.249, K.353, E.354 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.207, B:N.249, B:E.354

1 x K: POTASSIUM ION(Non-covalent)

K.5: 4 residues within 4Å: Chain B: Q.252, Q.253, L.255, Q.260 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:Q.253, B:L.255

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

CL.7: 1 residues within 4Å: Chain B: T.339 Ligand excluded by PLIP

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

FMT.8: 7 residues within 4Å: Chain B: F.184, F.200, E.201, T.202, V.224, S.225, S.226 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.224 Water bridges: B:A.230

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Herrera, A. et al., A Genomic Island of Vibrio cholerae Encodes a Three-Component Cytotoxin with Monomer and Protomer Forms Structurally Similar to Alpha-Pore-Forming Toxins. J.Bacteriol. (2022)

Release Date

2020-03-11

Peptides

Motility Associated Killing Factor E: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Motility Associated Killing Factor E