SMTL ID : 6dc3.1

RSV prefusion F bound to RSD5 Fab

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

SO4.1: 2 residues within 4Å: Chain A: R.67, R.87 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.87 SO4.2: 5 residues within 4Å: Chain B: V.109, G.111, Q.112, Y.144, K.170 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.111, B:Q.112, B:Y.144 Salt bridges: B:K.170 SO4.3: 3 residues within 4Å: Chain B: S.61, R.63, Q.81 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.61, B:Q.81 Salt bridges: B:R.63 SO4.4: 2 residues within 4Å: Chain B: S.69, G.70 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.70 SO4.5: 3 residues within 4Å: Chain B: G.70, N.71, T.72 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.71 SO4.6: 2 residues within 4Å: Chain B: P.7, A.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.8, B:S.9 SO4.7: 2 residues within 4Å: Chain B: A.161, G.162 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.162 SO4.8: 1 residues within 4Å: Chain B: R.56 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.56 SO4.11: 5 residues within 4Å: Chain C: I.206, K.209, S.213, I.214, S.215 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.213, C:S.215, C:S.215 Salt bridges: C:K.209 SO4.12: 4 residues within 4Å: Chain C: L.273, N.276, N.277, R.364 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.277 Salt bridges: C:R.364 SO4.13: 2 residues within 4Å: Chain C: L.193, D.194 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.194, C:D.194 Salt bridges: C:K.226 SO4.14: 4 residues within 4Å: Chain C: N.444, K.445, G.446, K.461 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.444, C:G.446, C:V.447 Salt bridges: C:K.461 SO4.15: 2 residues within 4Å: Chain C: T.174, N.175 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.174, C:T.174, C:N.175

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

NAG.9: 4 residues within 4Å: Chain C: N.27, T.29, K.42, G.43 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:K.42 NAG.10: 2 residues within 4Å: Chain C: N.500, A.504 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:A.504

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jones, H.G. et al., Alternative conformations of a major antigenic site on RSV F. Plos Pathog. (2019)

Release Date

2019-07-10

Peptides

Fab RSD5-Germline Heavy Chain: A
Fab RSD5-Germline Light Chain: B
RSV fusion glycoprotein: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
F

Fab RSD5-Germline Heavy Chain

Fab RSD5-Germline Light Chain

RSV fusion glycoprotein

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