SMTL ID : 4jf7.1

Structure of the parainfluenza virus 5 (PIV5) hemagglutinin-neuraminidase (HN) ectodomain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

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

NAG-NAG-MAN.1: 6 residues within 4Å: Chain A: P.181, G.182, Y.213, N.215, T.217, Q.317 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.317 Water bridges: A:Y.213, A:Y.213 NAG-NAG-MAN.2: 7 residues within 4Å: Chain A: S.428, E.429, N.452, N.453, T.454, Q.455, I.457 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.455

4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.3: 5 residues within 4Å: Chain B: Y.213, N.215, T.217, Q.317 Chain C: Q.57 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.317 NAG-NAG.4: 7 residues within 4Å: Chain B: S.428, E.429, N.452, N.453, T.454, Q.455, I.457 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 6 residues within 4Å: Chain B: E.56, Q.57 Chain C: Y.213, N.215, T.217, Q.317 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.317 NAG-NAG.6: 6 residues within 4Å: Chain D: E.429, N.452, N.453, T.454, Q.455, I.457 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.455

4 x CA: CALCIUM ION(Non-covalent)

CA.7: 4 residues within 4Å: Chain A: D.198, S.201, A.203, A.233 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.198, A:S.201, A:S.201, A:A.203, A:A.233, H2O.5 CA.10: 4 residues within 4Å: Chain B: D.198, S.201, A.203, A.233 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.198, B:S.201, B:S.201, B:A.203, B:A.233, H2O.10 CA.14: 4 residues within 4Å: Chain C: D.198, S.201, A.203, A.233 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.198, C:S.201, C:A.203 CA.17: 4 residues within 4Å: Chain D: D.198, S.201, A.203, A.233 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.198, D:S.201, D:S.201, D:A.203, D:A.233

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

SO4.8: 3 residues within 4Å: Chain A: R.353, R.443, Y.471 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.471 Salt bridges: A:R.353, A:R.443 SO4.12: 3 residues within 4Å: Chain B: R.353, R.443, Y.471 4 PLIP interactions: 4 interactions with chain B Water bridges: B:Y.471, B:Y.471 Salt bridges: B:R.353, B:R.443 SO4.15: 4 residues within 4Å: Chain C: R.111, R.353, R.443, Y.471 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.111, C:Y.471 Salt bridges: C:R.353, C:R.443 SO4.18: 4 residues within 4Å: Chain D: R.111, R.353, R.443, Y.471 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.111, D:R.111, D:Y.471 Salt bridges: D:R.353, D:R.443

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

NAG.9: 2 residues within 4Å: Chain A: A.83, N.87 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.87 NAG.11: 4 residues within 4Å: Chain B: A.83, E.84, N.87, S.513 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.87 NAG.13: 3 residues within 4Å: Chain B: L.55, Q.57, N.58 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.55 Hydrogen bonds: B:Q.57 NAG.16: 5 residues within 4Å: Chain C: E.429, N.452, T.454, Q.455, I.457 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:T.454 Hydrogen bonds: C:T.454 Water bridges: C:N.452, C:N.452 NAG.19: 1 residues within 4Å: Chain D: N.87 No protein-ligand interaction detected (PLIP) NAG.20: 6 residues within 4Å: Chain A: T.44, K.47 Chain D: Y.213, N.215, T.217, Q.317 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:P.181, D:T.217, D:T.217

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Welch, B.D. et al., Structure of the Parainfluenza Virus 5 (PIV5) Hemagglutinin-Neuraminidase (HN) Ectodomain. Plos Pathog. (2013)

Release Date

2013-09-04

Peptides

Hemagglutinin-neuraminidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
A

C
B

D
C

Hemagglutinin-neuraminidase