SMTL ID : 7bwu.1

Restructuring hemagglutinin-neuraminidase (HN) of Newcastle disease virus produced from Oryza sativa

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

homo-tetramer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: H.429, N.431, T.433 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.433 NAG.4: 3 residues within 4Å: Chain B: H.429, N.431, T.433 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.433, B:T.433 Water bridges: B:N.431, B:N.431 NAG.7: 3 residues within 4Å: Chain C: H.429, N.431, T.433 2 PLIP interactions: 2 interactions with chain C Water bridges: C:N.431, C:N.431 NAG.10: 3 residues within 4Å: Chain D: H.429, N.431, T.433 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.431, D:T.433 Water bridges: D:N.431

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: D.129, M.130, S.131, S.256, T.356 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.129 Water bridges: A:G.87, A:D.129, A:T.132, A:A.192, A:F.257, A:R.353 GOL.5: 5 residues within 4Å: Chain B: G.87, D.129, M.130, S.256, T.356 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.255 Water bridges: B:A.192, B:F.257, B:R.353 GOL.8: 6 residues within 4Å: Chain C: D.129, M.130, S.131, G.255, S.256, T.356 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:D.129 Water bridges: C:I.86, C:G.87, C:D.129, C:T.132, C:T.132, C:A.192, C:R.353, C:R.353 GOL.11: 6 residues within 4Å: Chain D: G.87, D.129, M.130, S.131, S.256, T.356 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.255 Water bridges: D:I.86, D:G.87, D:A.192, D:T.356

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.211, S.214, A.216, V.246 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:D.211, A:D.211, A:S.214, A:S.214, A:A.216, A:V.246 CA.6: 4 residues within 4Å: Chain B: D.211, S.214, A.216, V.246 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.211, B:D.211, B:S.214, B:S.214, B:V.246 CA.9: 4 residues within 4Å: Chain C: D.211, S.214, A.216, V.246 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.211, C:D.211, C:S.214, C:S.214, C:V.246 CA.12: 4 residues within 4Å: Chain D: D.211, S.214, A.216, V.246 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.211, D:D.211, D:S.214, D:A.216, D:V.246

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ma, F.S. et al., Restructuring a dimer antigen in transgenic rice system for high efficient B cell activation: Development of a super effective vaccine against Newcastle Disease Virus. To Be Published

Release Date

2021-04-21

Peptides

Hemagglutinin-neuraminidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

C
A

D
C

Hemagglutinin-neuraminidase