SMTL ID : 5cyb.1

Structure of a lipocalin lipoprotein affecting virulence in Streptococcus pneumoniae

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: D.80, W.96, E.98, K.108, I.121, D.124, K.126, I.148 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.96, A:E.98, A:K.108, A:D.124, A:D.124 GOL.7: 8 residues within 4Å: Chain B: D.80, W.96, E.98, K.108, I.121, D.124, K.126, I.148 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:W.96, B:E.98, B:K.108, B:D.124

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

ACT.2: 6 residues within 4Å: Chain A: N.133, K.152 Chain B: D.73, G.74, K.152 Ligands: CA.6 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.133 Water bridges: B:K.152 Salt bridges: B:K.152 ACT.8: 6 residues within 4Å: Chain A: D.73, G.74, K.152 Chain B: N.133, K.152 Ligands: CA.12 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.133 Water bridges: A:K.152 Salt bridges: A:K.152

8 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.80, D.81, S.145, D.146 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.81, A:D.81, H2O.1 CA.4: 2 residues within 4Å: Chain A: D.102, D.104 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.102, A:D.104, H2O.2 CA.5: 4 residues within 4Å: Chain A: D.139, D.141, D.143, D.146 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.141, H2O.1 CA.6: 4 residues within 4Å: Chain A: K.152 Chain B: D.71, D.73 Ligands: ACT.2 No protein-ligand interaction detected (PLIP) CA.9: 4 residues within 4Å: Chain B: D.80, D.81, S.145, D.146 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.81, B:D.81, H2O.3 CA.10: 2 residues within 4Å: Chain B: D.102, D.104 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.102, B:D.104, H2O.5 CA.11: 4 residues within 4Å: Chain B: D.139, D.141, D.143, D.146 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.141, H2O.3 CA.12: 4 residues within 4Å: Chain A: D.71, D.73 Chain B: K.152 Ligands: ACT.8 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abdullah, M.R. et al., Unraveling the function and structure of a lipocalin lipoprotein affecting virulence in Streptococcus pneumoniae. To Be Published

Release Date

2016-09-14

Peptides

Lipoprotein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Lipoprotein