SMTL ID : 4az5.1

Differential inhibition of the tandem GH20 catalytic modules in the pneumococcal exo-beta-D-N-acetylglucosaminidase, StrH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

homo-dimer

Ligands

2 x NGW: (2S,3aR,5R,6S,7R,7aR)-5-(hydroxymethyl)-2-methyl-2,3a,5,6,7,7a-hexahydro-1H-pyrano[3,2-d][1,3]thiazole-6,7-diol(Non-covalent)

NGW.1: 11 residues within 4Å: Chain A: R.16, H.117, D.180, E.181, F.235, W.259, Y.289, V.291, Y.302, W.337, D.339 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:D.180, A:F.235, A:W.259 Hydrogen bonds: A:R.16, A:R.16, A:D.180, A:D.180 NGW.10: 11 residues within 4Å: Chain B: R.16, H.117, D.180, E.181, F.235, W.259, Y.289, V.291, Y.302, W.337, D.339 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:D.180, B:F.235, B:W.259 Hydrogen bonds: B:R.16, B:R.16, B:D.180

8 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.3: 3 residues within 4Å: Chain A: H.228 Chain B: H.228 Ligands: MG.12 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:H.228, B:H.228, H2O.16, H2O.42 MG.8: 1 residues within 4Å: Ligands: MG.17 No protein-ligand interaction detected (PLIP) MG.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain A: H.228 Chain B: H.228 Ligands: MG.3 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:H.228, B:H.228, H2O.16, H2O.42 MG.17: 1 residues within 4Å: Ligands: MG.8 No protein-ligand interaction detected (PLIP) MG.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x PE4: 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL(Non-functional Binders)

PE4.4: 7 residues within 4Å: Chain A: Y.137, F.138, K.190, S.193, A.197, Y.201, Y.206 No protein-ligand interaction detected (PLIP) PE4.13: 7 residues within 4Å: Chain B: Y.137, F.138, K.190, S.193, A.197, Y.201, Y.206 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.137, B:Y.206

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

EDO.5: 4 residues within 4Å: Chain A: Y.200, N.242, S.243, D.244 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.243 Water bridges: A:Y.200 EDO.6: 3 residues within 4Å: Chain A: D.29, K.30, H.33 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.33 Water bridges: A:D.29, A:D.29, A:K.30 EDO.7: 3 residues within 4Å: Chain A: D.103, K.104, G.105 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.103 Water bridges: A:K.32 EDO.14: 4 residues within 4Å: Chain B: Y.200, N.242, S.243, D.244 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.243 Water bridges: B:D.244 EDO.15: 3 residues within 4Å: Chain B: D.29, K.30, H.33 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.33 Water bridges: B:D.29, B:K.30 EDO.16: 3 residues within 4Å: Chain B: D.103, K.104, G.105 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.103 Water bridges: B:K.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pluvinage, B. et al., Inhibition of the Family 20 Glycoside Hydrolase Catalytic Modules in the Streptococcus Pneumoniae Exo-Beta-D-N-Acetylglucosaminidase, Strh. Org.Biomol.Chem. (2013)

Release Date

2013-07-10

Peptides

BETA-N-ACETYLHEXOSAMINIDASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

BETA-N-ACETYLHEXOSAMINIDASE

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