SMTL ID : 5k6b.1

Crystal structure of prefusion-stabilized RSV F single-chain 9 DS-Cav1 variant.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.98 Å

Oligo State

homo-trimer

Ligands

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

NAG.1: 1 residues within 4Å: Chain A: N.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.2 NAG.6: 1 residues within 4Å: Chain B: N.2 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.2 NAG.11: 1 residues within 4Å: Chain C: N.2 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.2

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

SO4.2: 5 residues within 4Å: Chain A: R.173 Chain B: R.173 Chain C: R.173 Ligands: SO4.7, SO4.12 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C Salt bridges: A:R.173, B:R.173, C:R.173 SO4.3: 3 residues within 4Å: Chain A: T.275, D.276, R.277 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.276, A:R.277 Salt bridges: A:R.277 SO4.4: 4 residues within 4Å: Chain A: L.211, N.214, N.215, R.302 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.215 Salt bridges: A:R.302 SO4.5: 5 residues within 4Å: Chain A: K.436 Chain B: K.436 Chain C: K.436 Ligands: SO4.10, SO4.15 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Salt bridges: C:K.436, A:K.436, B:K.436 SO4.7: 5 residues within 4Å: Chain A: R.173 Chain B: R.173 Chain C: R.173 Ligands: SO4.2, SO4.12 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C Salt bridges: A:R.173, B:R.173, C:R.173 SO4.8: 3 residues within 4Å: Chain B: T.275, D.276, R.277 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.276, B:R.277 Salt bridges: B:R.277 SO4.9: 4 residues within 4Å: Chain B: L.211, N.214, N.215, R.302 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.215 Salt bridges: B:R.302 SO4.10: 5 residues within 4Å: Chain A: K.436 Chain B: K.436 Chain C: K.436 Ligands: SO4.5, SO4.15 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Salt bridges: C:K.436, A:K.436, B:K.436 SO4.12: 5 residues within 4Å: Chain A: R.173 Chain B: R.173 Chain C: R.173 Ligands: SO4.2, SO4.7 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C Salt bridges: A:R.173, B:R.173, C:R.173 SO4.13: 3 residues within 4Å: Chain C: T.275, D.276, R.277 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.276, C:R.277 Salt bridges: C:R.277 SO4.14: 4 residues within 4Å: Chain C: L.211, N.214, N.215, R.302 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.215 Salt bridges: C:R.302 SO4.15: 5 residues within 4Å: Chain A: K.436 Chain B: K.436 Chain C: K.436 Ligands: SO4.5, SO4.10 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Salt bridges: C:K.436, A:K.436, B:K.436

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joyce, M.G. et al., Iterative structure-based improvement of a fusion-glycoprotein vaccine against RSV. Nat.Struct.Mol.Biol. (2016)

Release Date

2016-08-31

Peptides

Fusion glycoprotein F0: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
F

C
F

Fusion glycoprotein F0