SMTL ID : 5k6i.1

Crystal structure of prefusion-stabilized RSV F single-chain 9-10 DS-Cav1 A149C-Y458C, S46G-E92D-S215P-K465Q variant.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.92 Å

Oligo State

homo-trimer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: E.35, K.127, D.130 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.35, A:E.35 ZN.2: 2 residues within 4Å: Chain A: K.251, H.253 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.253, H2O.1, H2O.1 ZN.8: 3 residues within 4Å: Chain B: E.35, K.127, D.130 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.35, B:E.35 ZN.9: 2 residues within 4Å: Chain B: K.251, H.253 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.253, H2O.2, H2O.2 ZN.15: 3 residues within 4Å: Chain C: E.35, K.127, D.130 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.35, C:E.35 ZN.16: 2 residues within 4Å: Chain C: K.251, H.253 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.253, H2O.3, H2O.3

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

EDO.3: 3 residues within 4Å: Chain A: K.112, S.195, D.199 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.112, A:K.112 EDO.4: 2 residues within 4Å: Chain A: D.246, R.300 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.300 EDO.10: 3 residues within 4Å: Chain B: K.112, S.195, D.199 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.112, B:K.112 EDO.11: 2 residues within 4Å: Chain B: D.246, R.300 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.300 EDO.17: 3 residues within 4Å: Chain C: K.112, S.195, D.199 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.112, C:K.112 EDO.18: 2 residues within 4Å: Chain C: D.246, R.300 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.300

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

PO4.5: 4 residues within 4Å: Chain A: E.57, K.60, Q.160 Chain B: Q.161 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.161, A:Q.160 Salt bridges: A:K.60 PO4.12: 4 residues within 4Å: Chain B: E.57, K.60, Q.160 Chain C: Q.161 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Q.160, C:Q.161 Salt bridges: B:K.60 PO4.19: 4 residues within 4Å: Chain A: Q.161 Chain C: E.57, K.60, Q.160 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Q.160, A:Q.161 Salt bridges: C:K.60

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

NAG.6: 1 residues within 4Å: Chain A: N.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.2 NAG.7: 1 residues within 4Å: Chain A: N.45 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.45 NAG.13: 1 residues within 4Å: Chain B: N.2 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.2 NAG.14: 1 residues within 4Å: Chain B: N.45 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.45 NAG.20: 1 residues within 4Å: Chain C: N.2 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.2 NAG.21: 1 residues within 4Å: Chain C: N.45 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.45

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

2016-08-17

Peptides

Fusion glycoprotein F0: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
F

C
F

Fusion glycoprotein F0