SMTL ID : 3zx7.1

Complex of lysenin with phosphocholine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.84 Å

Oligo State

monomer

Ligands

5 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 2 residues within 4Å: Chain A: E.83, E.84 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.83, A:E.84 PO4.2: 4 residues within 4Å: Chain A: E.6, R.168, K.195, G.296 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.6, A:G.296 Water bridges: A:R.168 Salt bridges: A:R.168 PO4.3: 5 residues within 4Å: Chain A: L.162, G.163, L.201, Y.202, E.203 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.201, A:E.203 PO4.4: 4 residues within 4Å: Chain A: E.203, D.204, W.205 Ligands: NA.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.203, A:E.203 PO4.5: 4 residues within 4Å: Chain A: H.171, E.173, D.288, K.289 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.173, A:K.289, A:K.289 Salt bridges: A:H.171

4 x PC: PHOSPHOCHOLINE(Non-covalent)

PC.6: 7 residues within 4Å: Chain A: R.183, K.184, S.226, Q.228, Y.232, P.276, Y.281 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.226, A:Y.232 Salt bridges: A:R.183, A:K.184 PC.10: 3 residues within 4Å: Chain A: T.237, D.238, N.239 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.237, A:D.238, A:N.239 Salt bridges: A:D.238 PC.11: 5 residues within 4Å: Chain A: H.80, S.81, I.132, D.133, E.134 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.81, A:E.134, A:E.134 Salt bridges: A:H.80, A:D.133 PC.12: 9 residues within 4Å: Chain A: S.225, S.226, D.227, G.229, F.265, S.268, C.282, L.283, D.284 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.225, A:S.225, A:S.226, A:S.268

3 x NA: SODIUM ION(Non-functional Binders)

NA.7: 3 residues within 4Å: Chain A: D.204, W.205 Ligands: PO4.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.205 NA.8: 3 residues within 4Å: Chain A: D.274, G.275, T.278 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.275, A:T.278 NA.9: 4 residues within 4Å: Chain A: Y.224, D.234, N.239, Q.242 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.234, A:Q.242

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

De Colibus, L. et al., Structures of Lysenin Reveal a Shared Evolutionary Origin for Pore-Forming Proteins and its Mode of Sphingomyelin Recognition. Structure (2012)

Release Date

2012-09-19

Peptides

LYSENIN: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

LYSENIN

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