SMTL ID : 4x36.1

Crystal structure of the autolysin LytA from Streptococcus pneumoniae TIGR4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: M.1, I.3, L.108, N.111, L.112, E.115 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.111, A:N.111 GOL.2: 3 residues within 4Å: Chain A: N.30, E.38, Y.41 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.30 Water bridges: A:T.28, A:N.37, A:E.38, A:Y.41 GOL.3: 3 residues within 4Å: Chain A: Q.18, P.19, D.68 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.68 Water bridges: A:Q.18 GOL.4: 4 residues within 4Å: Chain A: R.9, T.10, D.11, W.43 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.10, A:T.10, A:D.11, A:W.43 Water bridges: A:T.10 GOL.5: 7 residues within 4Å: Chain A: V.15, W.72, G.76, G.77, N.79, A.80 Ligands: GOL.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.72, A:N.79, A:A.80 Water bridges: A:G.16 GOL.6: 3 residues within 4Å: Chain A: E.48, W.72 Ligands: GOL.5 2 PLIP interactions: 2 interactions with chain A Water bridges: A:W.72, A:N.79 GOL.13: 6 residues within 4Å: Chain B: M.1, I.3, L.108, N.111, L.112, E.115 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.111, B:N.111 GOL.14: 3 residues within 4Å: Chain B: N.30, E.38, Y.41 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.30 Water bridges: B:T.28, B:N.37, B:E.38, B:Y.41 GOL.15: 3 residues within 4Å: Chain B: Q.18, P.19, D.68 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.68 Water bridges: B:Q.18, B:Y.83 GOL.16: 4 residues within 4Å: Chain B: R.9, T.10, D.11, W.43 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.10, B:T.10, B:D.11, B:W.43 GOL.17: 7 residues within 4Å: Chain B: V.15, W.72, G.76, G.77, N.79, A.80 Ligands: GOL.18 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:W.72, B:N.79, B:A.80 Water bridges: B:G.16 GOL.18: 3 residues within 4Å: Chain B: E.48, W.72 Ligands: GOL.17 2 PLIP interactions: 2 interactions with chain B Water bridges: B:W.72, B:N.79

2 x ZN: ZINC ION(Non-covalent)

ZN.7: 3 residues within 4Å: Chain A: H.26, H.133, D.149 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.26, A:H.133, A:D.149, H2O.3 ZN.19: 3 residues within 4Å: Chain B: H.26, H.133, D.149 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.26, B:H.133, B:D.149, H2O.12

10 x CHT: CHOLINE ION(Non-covalent)

CHT.8: 5 residues within 4Å: Chain A: W.220, W.228, Y.249, M.257, E.275 4 PLIP interactions: 4 interactions with chain A pi-Cation interactions: A:W.220, A:W.220, A:W.228, A:W.228 CHT.9: 4 residues within 4Å: Chain A: W.241, W.248, Y.264, Y.269 5 PLIP interactions: 5 interactions with chain A pi-Cation interactions: A:W.241, A:W.241, A:W.248, A:W.248, A:Y.264 CHT.10: 5 residues within 4Å: Chain A: W.261, W.268, Y.293, L.301 Chain B: D.312 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:D.312 pi-Cation interactions: A:W.261, A:W.261, A:W.268, A:W.268, A:Y.293 CHT.11: 5 residues within 4Å: Chain A: F.199, W.206, Y.229, M.237, E.254 2 PLIP interactions: 2 interactions with chain A pi-Cation interactions: A:F.199, A:W.206 CHT.12: 5 residues within 4Å: Chain A: N.181, W.186, Y.194, S.212, Y.214 2 PLIP interactions: 2 interactions with chain A pi-Cation interactions: A:W.186, A:W.186 CHT.20: 5 residues within 4Å: Chain B: W.220, W.228, Y.249, M.257, E.275 4 PLIP interactions: 4 interactions with chain B pi-Cation interactions: B:W.220, B:W.220, B:W.228, B:W.228 CHT.21: 4 residues within 4Å: Chain B: W.241, W.248, Y.264, Y.269 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.264 pi-Cation interactions: B:W.241, B:W.241, B:W.248, B:W.248, B:Y.264 CHT.22: 5 residues within 4Å: Chain A: D.312 Chain B: W.261, W.268, Y.293, L.301 5 PLIP interactions: 5 interactions with chain B pi-Cation interactions: B:W.261, B:W.261, B:W.268, B:W.268, B:Y.293 CHT.23: 5 residues within 4Å: Chain B: F.199, W.206, Y.229, M.237, E.254 2 PLIP interactions: 2 interactions with chain B pi-Cation interactions: B:F.199, B:W.206 CHT.24: 5 residues within 4Å: Chain B: N.181, W.186, Y.194, S.212, Y.214 2 PLIP interactions: 2 interactions with chain B pi-Cation interactions: B:W.186, B:W.186

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Q. et al., Full-length structure of the major autolysin LytA. Acta Crystallogr.,Sect.D (2015)

Release Date

2015-05-27

Peptides

Autolysin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Autolysin