SMTL ID : 6c0m.1

The synthesis, biological evaluation and structural insights of unsaturated 3-N-substituted sialic acids as probes of human parainfluenza virus-3 haemagglutinin-neuraminidase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.1: 5 residues within 4Å: Chain A: N.210, T.212, W.310, A.371, T.372 2 PLIP interactions: 2 interactions with chain A Water bridges: A:A.371, A:A.371

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.2: 3 residues within 4Å: Chain B: N.210, T.212, W.310 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.138, S.141, G.143, A.175 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.138, A:D.138, A:S.141, A:G.143, H2O.2 CA.10: 5 residues within 4Å: Chain B: D.138, S.141, S.142, G.143, A.175 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.138, B:S.141, B:G.143, B:A.175, H2O.11

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.4: 3 residues within 4Å: Chain A: R.381, N.382, T.384 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.384 Hydrogen bonds: A:T.384 NAG.11: 3 residues within 4Å: Chain B: R.381, N.382, T.384 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.382

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

EDO.5: 3 residues within 4Å: Chain A: S.357, Q.358, K.383 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.358 Water bridges: A:K.359, A:S.360, A:S.360 EDO.6: 4 residues within 4Å: Chain A: M.26, K.27, T.28, S.429 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.27, A:T.28, A:T.28, A:S.429 EDO.13: 10 residues within 4Å: Chain A: P.35, G.36 Chain B: P.43, T.44, T.45, G.48, L.68, I.69, T.70, Y.80 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.44, B:T.45, B:T.45, A:G.36

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 3 residues within 4Å: Chain A: E.321, P.323, H.326 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.326 SO4.12: 7 residues within 4Å: Chain A: H.411, K.412, S.413 Chain B: H.411, K.412, S.413, L.414 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.413, B:S.413, B:S.413, B:L.414, A:K.412, A:S.413, A:S.413 Water bridges: B:K.412, B:K.412 Salt bridges: B:H.411 SO4.15: 6 residues within 4Å: Chain B: N.107, I.108, N.109, D.110, R.112, R.162 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:N.107, B:I.108, B:N.109, B:N.109, B:D.110, B:D.110, B:D.110 Water bridges: B:R.112, B:T.160, B:T.160 Salt bridges: B:R.112, B:R.162

3 x 8LM: 2,6-anhydro-3,5-dideoxy-5-[(2-methylpropanoyl)amino]-3-(4-phenyl-1H-1,2,3-triazol-1-yl)-D-glycero-D-galacto-non-2-enoni c acid(Non-covalent)

8LM.8: 12 residues within 4Å: Chain A: C.49, R.51, T.52, C.73, E.135, Y.178, Y.196, E.268, R.283, R.361, E.408, F.417 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Y.178, A:F.417 Hydrogen bonds: A:R.51, A:R.51, A:E.135, A:Y.196, A:Y.196, A:R.283 Water bridges: A:T.52, A:T.52, A:S.267, A:E.268, A:R.283, A:R.283, A:E.408 Salt bridges: A:R.283, A:R.361 pi-Cation interactions: A:R.51 8LM.9: 15 residues within 4Å: Chain A: P.37, G.38, L.39, T.89, V.90, N.91, D.97, L.98, N.99, R.101 Chain B: V.82, I.102, S.103, H.104, T.105 15 PLIP interactions: 6 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:V.82, B:I.102, A:P.37, A:P.37, A:L.39 Hydrogen bonds: B:S.103, B:T.105, A:T.89, A:T.89, A:N.91, A:N.99, A:R.101 Water bridges: B:S.103, B:H.104, A:S.92 8LM.16: 14 residues within 4Å: Chain B: C.49, V.50, R.51, T.52, C.73, S.114, E.135, Y.178, Y.196, E.268, R.283, R.361, E.408, F.417 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:R.51, B:Y.178, B:F.417 Hydrogen bonds: B:R.51, B:R.51, B:E.135, B:Y.196, B:Y.196, B:R.283 Water bridges: B:T.52, B:T.52, B:E.135, B:E.268, B:R.283, B:R.283, B:T.285 Salt bridges: B:R.283, B:R.361 pi-Stacking: B:F.417 pi-Cation interactions: B:R.51

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 2 residues within 4Å: Chain B: I.1, R.101 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pascolutti, M. et al., Structural Insights into Human Parainfluenza Virus 3 Hemagglutinin-Neuraminidase Using Unsaturated 3- N-Substituted Sialic Acids as Probes. ACS Chem. Biol. (2018)

Release Date

2018-06-27

Peptides

Hemagglutinin-neuraminidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Hemagglutinin-neuraminidase