SMTL ID : 4mze.1

Crystal structure of hPIV3 hemagglutinin-neuraminidase, H552Q/Q559R mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]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-MAN-MAN-MAN-MAN.1: 5 residues within 4Å: Chain A: N.216, T.218, W.316, S.377, T.378 No protein-ligand interaction detected (PLIP)

1 x NAG- FUL: beta-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUL.2: 3 residues within 4Å: Chain A: R.387, N.388, T.390 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.388 Water bridges: A:N.388

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN.3: 4 residues within 4Å: Chain B: T.167, R.168, F.169, N.173 No protein-ligand interaction detected (PLIP)

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.4: 3 residues within 4Å: Chain B: N.216, T.218, W.316 No protein-ligand interaction detected (PLIP)

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

NAG.5: 4 residues within 4Å: Chain A: T.167, R.168, F.169, N.173 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.167, A:F.169 NAG.19: 3 residues within 4Å: Chain B: R.387, N.388, T.390 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.388, B:T.390

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 6 residues within 4Å: Chain A: R.57, T.58, E.274, R.289, Y.343, Y.395 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.274, A:E.274 Water bridges: A:R.57, A:R.289, A:Y.343 Salt bridges: A:R.57, A:R.289 PO4.20: 6 residues within 4Å: Chain B: R.57, T.58, E.274, R.289, Y.343, Y.395 8 PLIP interactions: 8 interactions with chain B Water bridges: B:R.57, B:R.289, B:R.289, B:R.367, B:G.394, B:E.414 Salt bridges: B:R.57, B:R.289 PO4.21: 5 residues within 4Å: Chain A: Q.417, K.418, S.419 Chain B: K.418, S.419 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:Q.417, A:K.418, A:S.419, A:S.419, B:S.419, B:S.419, B:S.419, B:S.419 Water bridges: B:K.418

2 x CA: CALCIUM ION(Non-covalent)

CA.7: 4 residues within 4Å: Chain A: D.144, S.147, G.149, A.181 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.144, A:D.144, A:S.147, A:S.147, A:G.149 CA.22: 4 residues within 4Å: Chain B: D.144, S.147, G.149, A.181 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.144, B:S.147, B:G.149, B:A.181, H2O.15

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

EDO.8: 6 residues within 4Å: Chain A: V.62, A.124, L.125, G.190, I.191, Y.192 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.125, A:Y.192 Water bridges: A:Y.192 EDO.9: 6 residues within 4Å: Chain A: W.330, D.362, S.363, Q.364, R.380 Ligands: PEG.17 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.364, A:R.380 Water bridges: A:R.380, A:R.380 EDO.10: 3 residues within 4Å: Chain A: R.267, Q.268, R.311 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.268, A:R.311, A:R.311 EDO.11: 6 residues within 4Å: Chain A: Y.86, T.111, N.113, I.114 Chain B: P.41, G.42 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:I.114, B:P.41 Water bridges: B:N.97, B:D.99 EDO.12: 9 residues within 4Å: Chain A: E.141, Y.145, Y.202, F.237, M.242, W.271, G.272, S.273, T.291 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.272, A:T.291 Water bridges: A:E.274 EDO.13: 3 residues within 4Å: Chain A: M.32, K.33, T.34 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.33, A:T.34, A:T.34 EDO.14: 5 residues within 4Å: Chain A: S.120, E.141, Y.184, Y.202 Ligands: PEG.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.120, A:E.141 EDO.15: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.219 EDO.23: 6 residues within 4Å: Chain B: V.62, A.124, L.125, G.190, I.191, Y.192 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.125, B:Y.192 Water bridges: B:Y.192, B:L.279 EDO.24: 7 residues within 4Å: Chain B: L.126, Y.131, G.195, K.196, I.197, V.249, K.251 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.197, B:V.249 Water bridges: B:G.195, B:K.251 EDO.25: 6 residues within 4Å: Chain B: W.330, D.362, S.363, Q.364, R.380 Ligands: PEG.30 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.364, B:R.380 EDO.26: 5 residues within 4Å: Chain B: L.126, N.127, T.128, D.129, H.160 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.127, B:T.128, B:T.128, B:D.129 EDO.27: 2 residues within 4Å: Chain B: T.352, S.354 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.352, B:S.354 Water bridges: B:N.350, B:S.377 EDO.28: 3 residues within 4Å: Chain B: E.141, Y.184, Y.202 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.120, B:E.141, B:Y.202 EDO.29: 5 residues within 4Å: Chain B: N.369, A.385, R.387, N.388, K.389 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.369, B:K.389

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.16: 6 residues within 4Å: Chain A: Q.80, D.81, K.119, P.137 Ligands: EDO.14, SO4.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.81, A:V.139 PEG.17: 6 residues within 4Å: Chain A: D.362, S.363, Q.364, V.368, K.389 Ligands: EDO.9 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.362, A:Q.364, A:K.389 Water bridges: A:K.365, A:K.365, A:S.366, A:S.366 PEG.30: 6 residues within 4Å: Chain B: D.362, S.363, Q.364, V.368, K.389 Ligands: EDO.25 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.362, B:Q.364 Water bridges: B:K.365, B:N.369 PEG.31: 11 residues within 4Å: Chain B: E.141, Y.145, Y.202, F.237, M.242, W.271, G.272, S.273, E.274, R.289, T.291 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.141, B:Y.145, B:E.274, B:R.289

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

SO4.18: 3 residues within 4Å: Chain A: R.57, Q.80 Ligands: PEG.16 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.79, A:Q.80 Salt bridges: A:R.57

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, R. et al., Interaction between the hemagglutinin-neuraminidase and fusion glycoproteins of human parainfluenza virus type III regulates viral growth in vivo. MBio (2013)

Release Date

2013-11-06

Peptides

Hemagglutinin-neuraminidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Hemagglutinin-neuraminidase