SMTL ID : 2ww5.1

3D-STRUCTURE OF THE MODULAR AUTOLYSIN LYTC FROM STREPTOCOCCUS PNEUMONIAE AT 1.6 A RESOLUTION

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

monomer

Ligands

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: N.72, R.76, Y.77, S.78, E.81 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.72, A:E.81 Water bridges: A:R.76, A:Y.77, A:S.78, A:Q.79 GOL.2: 2 residues within 4Å: Chain A: W.135, Y.137 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.137 GOL.3: 4 residues within 4Å: Chain A: 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.4: 4 residues within 4Å: Chain A: W.122, Q.144, Y.147 Ligands: CHT.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.144 Water bridges: A:Y.131 GOL.5: 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.6: 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.7: 4 residues within 4Å: Chain A: Y.302, Y.331, Y.369, V.370 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.370

7 x CHT: CHOLINE ION(Non-covalent)

CHT.8: 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.9: 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:D.114 pi-Cation interactions: A:W.59, A:W.59, A:W.68, A:W.68, A:Y.86 CHT.10: 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.11: 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.12: 6 residues within 4Å: Chain A: W.122, W.129, Y.147, M.155, D.175 Ligands: GOL.4 5 PLIP interactions: 5 interactions with chain A Water bridges: A:Y.147 pi-Cation interactions: A:W.122, A:W.122, A:W.129, A:W.129 CHT.13: 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.14: 6 residues within 4Å: Chain A: W.160, Y.169, Y.191, M.199, R.201, S.213 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.201 pi-Cation interactions: A:W.160, A:W.160, A:Y.169

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

CL.15: 4 residues within 4Å: Chain A: N.85, A.116, Y.117, H.119 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain A: Y.407, R.408, S.409, A.428 Ligand excluded by PLIP

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

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