SMTL ID : 2yl8.1

Inhibition of the pneumococcal virulence factor StrH and molecular insights into N-glycan recognition and hydrolysis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

1 x MAN- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose(Non-covalent)

MAN-NAG.1: 14 residues within 4Å: Chain A: R.16, H.117, D.180, Q.181, N.184, A.189, F.235, W.259, W.263, Y.289, V.291, Y.302, W.337, D.339 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Q.181, A:N.184, A:N.184, A:Y.302, A:D.339, A:R.16, A:R.16, A:H.117, A:D.180, A:D.180 Water bridges: A:D.286, A:D.339, A:N.45, A:Q.181, A:R.294, A:D.339, A:D.339 Hydrophobic interactions: A:F.235, A:W.259

9 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 1 residues within 4Å: Chain A: D.149 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.149, H2O.10, H2O.10, H2O.10, H2O.10, H2O.14 MN.3: 2 residues within 4Å: Chain A: D.297, D.305 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.297, A:D.305, H2O.17, H2O.18 MN.4: 2 residues within 4Å: Chain A: N.242, D.267 No protein-ligand interaction detected (PLIP) MN.5: 1 residues within 4Å: Chain A: D.79 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.79, H2O.5, H2O.5, H2O.5, H2O.5, H2O.24 MN.6: 1 residues within 4Å: Chain A: D.67 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.67, H2O.4, H2O.24 MN.7: 1 residues within 4Å: Chain A: D.405 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.405 MN.8: 4 residues within 4Å: Chain A: E.370, E.373 Ligands: MN.9, MN.10 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.370, A:E.373 MN.9: 2 residues within 4Å: Chain A: E.370 Ligands: MN.8 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.370, H2O.2, H2O.21 MN.10: 2 residues within 4Å: Chain A: E.370 Ligands: MN.8 No protein-ligand interaction detected (PLIP)

2 x 15P: POLYETHYLENE GLYCOL (N=34)(Non-functional Binders)

15P.11: 8 residues within 4Å: Chain A: Y.137, F.138, S.193, V.194, A.197, Y.201, E.204, Y.206 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.206 15P.12: 4 residues within 4Å: Chain A: Y.200, N.242, S.243, D.244 No protein-ligand interaction detected (PLIP)

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

EDO.13: 7 residues within 4Å: Chain A: F.135, D.147, L.148, D.149, Y.182, L.195, P.207 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.148, A:D.149, A:Y.182

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pluvinage, B. et al., Inhibition of the Pneumococcal Virulence Factor Strh and Molecular Insights Into N-Glycan Recognition and Hydrolysis. Structure (2011)

Release Date

2011-09-07

Peptides

BETA-N-ACETYLHEXOSAMINIDASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

BETA-N-ACETYLHEXOSAMINIDASE