SMTL ID : 4cdb.1

Crystal structure of listeriolysin O

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

monomer

Ligands

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 3 residues within 4Å: Chain A: Q.392, K.444, W.454 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.444 Salt bridges: A:K.444 ACT.2: 7 residues within 4Å: Chain A: N.394, N.440, V.441, Y.442, D.459, D.460, R.461 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.440, A:Y.442, A:R.461 ACT.3: 5 residues within 4Å: Chain A: L.30, Y.32, K.355, D.356 Ligands: NA.15 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.32, A:D.356 Water bridges: A:D.31 Salt bridges: A:K.355 ACT.4: 3 residues within 4Å: Chain A: E.176, K.188 Ligands: NA.18 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.191 Salt bridges: A:K.188

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

NA.5: 3 residues within 4Å: Chain A: D.169, D.170, K.182 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.169, A:D.170, A:K.182, A:K.182 NA.6: 4 residues within 4Å: Chain A: Y.174, I.201, Q.207, T.371 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.207 Water bridges: A:S.373, A:S.373 NA.7: 3 residues within 4Å: Chain A: I.180, G.184, N.364 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.185, A:N.364, A:N.364 NA.8: 2 residues within 4Å: Chain A: Y.402, E.408 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.402, A:Y.402 Water bridges: A:R.51 NA.9: 3 residues within 4Å: Chain A: S.85, T.87, N.141 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.141, A:N.141 NA.10: 3 residues within 4Å: Chain A: E.171, Q.178, Y.368 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.171, A:Q.178, A:Y.368 NA.11: 4 residues within 4Å: Chain A: K.110, R.111, N.134, T.136 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.111, A:N.134, A:N.134 NA.12: 4 residues within 4Å: Chain A: Y.88, R.111, A.135, T.136 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.88, A:R.111, A:A.135 Water bridges: A:L.92, A:K.137 NA.13: 3 residues within 4Å: Chain A: Q.78, F.183, Y.265 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.183 Water bridges: A:S.212 NA.14: 2 residues within 4Å: Chain A: V.109, Q.240 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.240 Water bridges: A:Q.240 NA.15: 5 residues within 4Å: Chain A: Y.32, F.353, K.355, D.356 Ligands: ACT.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.32 NA.16: 6 residues within 4Å: Chain A: Y.168, D.170, E.209, I.211, F.281, D.282 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.170, A:D.170, A:K.278 NA.17: 4 residues within 4Å: Chain A: D.43, S.175, E.176, S.177 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.43, A:E.176, A:S.177 NA.18: 4 residues within 4Å: Chain A: E.176, K.188, N.191 Ligands: ACT.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.176, A:E.176, A:N.191 NA.19: 1 residues within 4Å: Chain A: Y.310 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.193, A:Y.310, A:Y.310

1 x TAM: TRIS(HYDROXYETHYL)AMINOMETHANE(Non-covalent)

TAM.20: 6 residues within 4Å: Chain A: T.456, V.457, I.458, D.459, D.460, Y.482 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.456, A:D.459, A:D.460, A:Y.482

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koester, S. et al., Crystal Structure of Listeriolysin O Reveals Molecular Details of Oligomerization and Pore Formation. Nat.Commun. (2014)

Release Date

2014-04-23

Peptides

LISTERIOLYSIN O: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

LISTERIOLYSIN O