SMTL ID : 4zgh.1

Structure of Sugar Binding Protein Pneumolysin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

monomer

Ligands

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 10 residues within 4Å: Chain A: Y.78, L.96, L.97, A.98, V.99, D.100, R.101, D.124, P.125, S.126 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.99 EDO.2: 6 residues within 4Å: Chain A: H.5, A.102, P.103, F.221, Q.222, D.223 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.223 EDO.3: 5 residues within 4Å: Chain A: A.377, T.465, T.466, L.467, Y.468 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.465, A:T.466 EDO.4: 1 residues within 4Å: Chain A: D.100 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.100 EDO.5: 4 residues within 4Å: Chain A: Y.22, D.23, K.24, K.25 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.22, A:K.24, A:K.25 Water bridges: A:K.24

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 8 residues within 4Å: Chain A: S.375, G.376, A.377, W.463, G.464, T.465, Y.468, Q.470 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.375, A:G.464, A:Q.470 PEG.7: 5 residues within 4Å: Chain A: V.379, D.410, W.443 Ligands: AUC.8, AUC.9 No protein-ligand interaction detected (PLIP)

2 x AUC: GOLD (I) CYANIDE ION(Non-covalent)

AUC.8: 5 residues within 4Å: Chain A: C.435, G.437, W.442 Ligands: PEG.7, AUC.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.437 AUC.9: 4 residues within 4Å: Chain A: V.379, C.435 Ligands: PEG.7, AUC.8 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.435

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lawrence, S.L. et al., Crystal structure of Streptococcus pneumoniae pneumolysin provides key insights into early steps of pore formation. Sci Rep (2015)

Release Date

2016-03-09

Peptides

Pneumolysin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Pneumolysin