SMTL ID : 4wef.1

Structure of the Hemagglutinin-neuraminidase from Human parainfluenza virus type III: complex with difluorosialic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA- BMA: beta-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-BMA.1: 7 residues within 4Å: Chain A: N.210, T.212, W.310, T.370, A.371, T.372 Ligands: SO4.12 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.370, A:T.370, A:T.372 Water bridges: A:A.371, A:A.371 NAG-NAG-BMA-BMA.3: 4 residues within 4Å: Chain B: N.210, T.212, W.310, T.372 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.372

2 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.2: 8 residues within 4Å: Chain A: L.381, N.382, T.384 Chain B: D.47, K.412, S.413, L.414, N.415 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.4: 9 residues within 4Å: Chain A: V.46, D.47, S.413, L.414 Chain B: L.381, N.382, T.384, K.412 Ligands: SO4.26 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.413, A:N.415 Hydrophobic interactions: A:V.46, A:D.47, A:L.414, B:L.381

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

NAG.5: 2 residues within 4Å: Chain A: R.162, N.167 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.166, A:N.167 Water bridges: A:N.167 NAG.18: 3 residues within 4Å: Chain B: R.162, N.166, N.167 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.166

2 x FSI: 5-acetamido-3,5-dideoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulopyranosonic acid(Post Translational Modification)

FSI.6: 10 residues within 4Å: Chain A: R.51, T.52, E.135, Y.178, Y.196, E.268, R.283, R.361, Y.389 Ligands: DF4.7 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.178 Hydrogen bonds: A:E.135, A:Y.196, A:Y.196, A:R.283 Water bridges: A:E.268, A:E.268, A:R.283, A:R.283 Salt bridges: A:R.51, A:R.283, A:R.361 FSI.19: 9 residues within 4Å: Chain B: R.51, E.135, Y.178, Y.196, E.268, R.283, R.361, Y.389 Ligands: DF4.20 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Y.178 Hydrogen bonds: B:Y.196, B:E.268, B:E.268, B:R.283 Water bridges: B:E.268, B:R.283, B:R.283 Salt bridges: B:R.51, B:R.283, B:R.361

2 x DF4: (3R,4R,5R,6R)-5-(acetylamino)-3-fluoro-4-hydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]-3,4,5,6-tetrahydropyranium-2-carboxylate(Non-covalent)

DF4.7: 11 residues within 4Å: Chain A: R.51, E.135, Y.178, Y.196, E.268, R.283, T.285, R.361, Y.389 Ligands: FSI.6, SFJ.9 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.178 Hydrogen bonds: A:Y.196, A:Y.196, A:R.283, A:T.285 Water bridges: A:E.268, A:E.268, A:R.283, A:R.283 Salt bridges: A:R.51, A:R.283, A:R.361 DF4.20: 9 residues within 4Å: Chain B: R.51, E.135, Y.178, Y.196, E.268, R.283, R.361, Y.389 Ligands: FSI.19 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:Y.178 Hydrogen bonds: B:Y.196, B:Y.196, B:R.283, B:Y.389, B:Y.389 Water bridges: B:E.135, B:R.283, B:R.283, B:T.285, B:T.285 Salt bridges: B:R.51, B:R.283, B:R.361

3 x SFJ: (2R,3R,4R,5R,6R)-5-acetamido-2,3-difluoro-4-hydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]tetrahydro-2H-pyran-2-carboxylic acid(Non-covalent)

SFJ.8: 7 residues within 4Å: Chain A: L.120, N.121, T.122, D.123, N.153, K.245 Ligands: SO4.15 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.153 Water bridges: A:N.121, A:T.122, A:T.122 SFJ.9: 7 residues within 4Å: Chain A: R.51, C.73, Q.74, R.361, A.387, N.410 Ligands: DF4.7 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.74, A:R.361, A:A.387, A:A.387, A:N.410 Salt bridges: A:R.51 SFJ.21: 8 residues within 4Å: Chain B: K.217, D.221, Q.224, A.225, P.229, E.321, D.330, G.331 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:E.321 Hydrogen bonds: B:K.217, B:D.330, B:G.331, B:G.331 Water bridges: B:K.217 Halogen bonds: B:Q.224

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

SO4.10: 3 residues within 4Å: Chain A: R.261, Q.262, R.305 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.262 Salt bridges: A:R.261, A:R.305 SO4.11: 4 residues within 4Å: Chain A: H.104, T.105 Chain B: N.91, S.92 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.92, A:T.105, A:T.105 Water bridges: B:D.93 Salt bridges: A:H.104 SO4.12: 4 residues within 4Å: Chain A: N.344, T.346, S.348 Ligands: NAG-NAG-BMA-BMA.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.344, A:T.346, A:S.348 Water bridges: A:T.346 SO4.13: 4 residues within 4Å: Chain A: N.91, S.92 Chain B: H.104, T.105 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.92, B:T.105 Water bridges: A:N.91, A:D.97, B:T.105 Salt bridges: B:H.104 SO4.14: 3 residues within 4Å: Chain A: M.26, K.27, T.28 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.27, A:T.28, A:T.28 Salt bridges: A:K.27 SO4.15: 3 residues within 4Å: Chain A: N.121, Y.186 Ligands: SFJ.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.121, A:Y.186 Water bridges: A:N.121 SO4.17: 6 residues within 4Å: Chain A: H.411, K.412, S.413 Chain B: H.411, K.412, S.413 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:H.411, A:S.413, A:S.413, B:K.412, B:S.413, B:S.413, B:S.413 Salt bridges: A:H.411 SO4.22: 3 residues within 4Å: Chain B: R.261, Q.262, R.305 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.262 Water bridges: B:S.259, B:R.305 Salt bridges: B:R.261, B:R.305 SO4.23: 2 residues within 4Å: Chain B: S.20, G.21 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.21 SO4.24: 2 residues within 4Å: Chain B: S.429, C.430 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:C.430 Water bridges: B:K.400 SO4.25: 3 residues within 4Å: Chain B: P.142, E.200, R.234 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.234 SO4.26: 3 residues within 4Å: Chain B: N.382, R.383 Ligands: NAG-NAG-FUC.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.383 Water bridges: B:N.363 SO4.27: 3 residues within 4Å: Chain B: S.357, Q.358, R.383 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.358 Water bridges: B:S.357, B:K.359 Salt bridges: B:R.383

2 x CA: CALCIUM ION(Non-covalent)

CA.16: 5 residues within 4Å: Chain A: D.138, S.141, P.142, G.143, A.175 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.138, A:D.138, A:S.141, A:G.143, A:A.175 CA.28: 5 residues within 4Å: Chain B: D.138, S.141, P.142, G.143, A.175 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.138, B:D.138, B:S.141, B:G.143, B:A.175

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Streltsov, V.A. et al., Catalytic mechanism and novel receptor binding sites of human parainfluenza virus type 3 hemagglutinin-neuraminidase (hPIV3 HN). Antiviral Res. (2015)

Release Date

2015-09-16

Peptides

Hemagglutinin-neuraminidase glycoprotein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Hemagglutinin-neuraminidase glycoprotein