SMTL ID : 2wwc.1

3D-structure of the modular autolysin LytC from Streptococcus pneumoniae in complex with synthetic peptidoglycan ligand

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: Y.41, W.42, D.62, Y.64, Y.65 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.42, A:W.42 GOL.2: 6 residues within 4Å: Chain A: N.72, D.74, R.76, Y.77, Q.79, E.81 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.74, A:R.76, A:Q.79, A:E.81 Water bridges: A:D.45, A:N.72, A:S.73, A:Y.77, A:Q.79 GOL.3: 2 residues within 4Å: Chain A: I.100, Y.101 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.101 Water bridges: A:N.80, A:Y.87 GOL.4: 2 residues within 4Å: Chain A: W.135, Y.137 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.137 GOL.5: 5 residues within 4Å: Chain A: Y.117, H.119, Q.120, K.134, W.135 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.135 Water bridges: A:N.85, A:Y.117, A:Q.120 GOL.6: 5 residues within 4Å: Chain A: W.122, Q.144, G.145, S.146, Y.147 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.144, A:S.146, A:S.146 GOL.7: 5 residues within 4Å: Chain A: L.124, N.127, K.128, W.129, Q.157 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.127, A:Q.157, A:Q.157 Water bridges: A:W.129 GOL.8: 5 residues within 4Å: Chain A: Q.142, W.143, D.163, A.165, Y.166 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.143, A:W.143 Water bridges: A:W.143 GOL.9: 4 residues within 4Å: Chain A: W.204, G.206, N.207, L.236 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.207 GOL.10: 4 residues within 4Å: Chain A: R.253, E.266, H.267, D.294 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.266, A:D.294 Water bridges: A:R.253, A:R.253 GOL.11: 5 residues within 4Å: Chain A: H.267, K.269, E.444, W.467, Y.468 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.269, A:K.269, A:Y.468 Water bridges: A:T.265, A:Y.468 GOL.12: 5 residues within 4Å: Chain A: N.258, Y.430, Y.449, T.450, S.452 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.258, A:T.450, A:T.450 Water bridges: A:N.258, A:T.431, A:T.431, A:T.431, A:S.452 GOL.13: 4 residues within 4Å: Chain A: K.269, S.357, Y.358, E.444 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.444 Water bridges: A:S.357, A:Y.358, A:N.401, A:E.444, A:W.467 GOL.14: 6 residues within 4Å: Chain A: D.273, D.363, Q.365, Y.405, Q.448, D.463 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.365, A:Y.405, A:Y.405, A:Q.448 Water bridges: A:D.363

8 x CHT: CHOLINE ION(Non-covalent)

CHT.15: 6 residues within 4Å: Chain A: W.42, Y.65, F.69, Y.77, G.91, Y.93 3 PLIP interactions: 3 interactions with chain A pi-Cation interactions: A:W.42, A:W.42, A:Y.77 CHT.16: 5 residues within 4Å: Chain A: W.59, W.68, Y.86, M.94, D.114 6 PLIP interactions: 6 interactions with chain A Water bridges: A:Y.86 pi-Cation interactions: A:W.59, A:W.59, A:W.68, A:W.68, A:Y.86 CHT.17: 6 residues within 4Å: Chain A: W.82, G.84, Y.105, F.109, Y.117, W.135 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.84 Water bridges: A:Y.117 pi-Cation interactions: A:W.82, A:W.82 CHT.18: 5 residues within 4Å: Chain A: W.99, W.108, Y.130, M.138, Q.152 4 PLIP interactions: 4 interactions with chain A pi-Cation interactions: A:W.99, A:W.99, A:W.108, A:W.108 CHT.19: 5 residues within 4Å: Chain A: W.122, W.129, Y.147, M.155, D.175 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:W.129 Water bridges: A:Y.147 pi-Cation interactions: A:W.122, A:W.122, A:W.129, A:W.129 CHT.20: 6 residues within 4Å: Chain A: W.143, G.145, Y.166, F.170, Y.178, W.196 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.145 pi-Cation interactions: A:W.143, A:Y.166, A:Y.178 CHT.21: 5 residues within 4Å: Chain A: W.160, Y.169, Y.191, M.199, S.213 3 PLIP interactions: 3 interactions with chain A pi-Cation interactions: A:W.160, A:W.160, A:Y.169 CHT.22: 4 residues within 4Å: Chain A: Y.302, Y.331, Y.369, V.370 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:Y.369

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Perez-Dorado, I. et al., Insights Into Pneumococcal Fratricide from the Crystal Structures of the Modular Killing Factor Lytc. Nat.Struct.Mol.Biol. (2010)

Release Date

2010-04-21

Peptides

1,4-BETA-N-ACETYLMURAMIDASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

1,4-BETA-N-ACETYLMURAMIDASE