SMTL ID : 4mza.1

Crystal structure of hPIV3 hemagglutinin-neuraminidase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-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-MAN-MAN-MAN-MAN-MAN.1: 6 residues within 4Å: Chain A: N.216, T.218, W.316, T.376, S.377, T.378 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN: 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.2: 3 residues within 4Å: Chain B: T.167, R.168, 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.3: 2 residues within 4Å: Chain B: N.216, W.316 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.4: 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

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.6: 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

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: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.144, A:S.147, A:G.149, A:A.181, H2O.4 CA.12: 4 residues within 4Å: Chain B: D.144, S.147, G.149, A.181 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.144, B:S.147, B:S.147, B:G.149, B:A.181

5 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.125, A:Y.192 EDO.10: 6 residues within 4Å: Chain A: W.330, D.362, S.363, Q.364, R.380 Ligands: EDO.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.364, A:R.380 Water bridges: A:R.380 EDO.11: 4 residues within 4Å: Chain A: S.363, Q.364, V.368 Ligands: EDO.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.364 Water bridges: A:S.366, A:S.366, A:S.366 EDO.16: 6 residues within 4Å: Chain B: V.62, A.124, L.125, G.190, I.191, Y.192 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.125, B:Y.192 Water bridges: B:Y.192 EDO.17: 5 residues within 4Å: Chain B: W.330, D.362, S.363, Q.364, R.380 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.364, B:R.380 Water bridges: B:R.380

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

SO4.9: 3 residues within 4Å: Chain A: M.32, K.33, T.34 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.33, A:T.34, A:T.34 Water bridges: A:S.435, A:S.435, A:S.435 SO4.15: 4 residues within 4Å: Chain B: H.403, Y.404, N.405, K.406 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.405, B:N.405, B:K.406 Salt bridges: B:K.406

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

PO4.13: 7 residues within 4Å: Chain A: H.417, K.418, S.419 Chain B: H.417, K.418, S.419, L.420 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:S.419, B:S.419, B:L.420, A:K.418, A:S.419 Water bridges: B:K.418, A:H.417, A:S.419 Salt bridges: B:H.417, A:H.417 PO4.14: 2 residues within 4Å: Chain B: R.289, R.367 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.289, B:R.289 Salt bridges: B:R.289, B:R.367

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