SMTL ID : 5c6b.1

Crystal Structure of Prefusion-stabilized RSV F variant SC-TM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-hexamer

Ligands

6 x NHE: 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID(Non-covalent)

NHE.1: 8 residues within 4Å: Chain A: F.340, F.430, Y.431, D.432, V.435, N.449, I.452, L.456 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.340, A:F.430, A:Y.431 Hydrogen bonds: A:D.432, A:N.449 NHE.8: 8 residues within 4Å: Chain B: F.340, F.430, Y.431, D.432, V.435, N.449, I.452, L.456 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.340, B:F.430, B:Y.431 Hydrogen bonds: B:D.432, B:N.449 Water bridges: B:D.432, B:D.432 NHE.15: 8 residues within 4Å: Chain C: F.340, F.430, Y.431, D.432, V.435, N.449, I.452, L.456 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.340, C:F.430, C:Y.431 Hydrogen bonds: C:D.432, C:N.449 Water bridges: C:D.432, C:D.432 NHE.22: 8 residues within 4Å: Chain D: F.340, F.430, Y.431, D.432, V.435, N.449, I.452, L.456 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:F.340, D:F.430, D:Y.431 Hydrogen bonds: D:D.432, D:N.449 Water bridges: D:D.432, D:D.432 NHE.29: 8 residues within 4Å: Chain E: F.340, F.430, Y.431, D.432, V.435, N.449, I.452, L.456 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:F.340, E:F.430, E:Y.431 Hydrogen bonds: E:D.432, E:N.449 NHE.36: 8 residues within 4Å: Chain F: F.340, F.430, Y.431, D.432, V.435, N.449, I.452, L.456 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:F.340, F:F.430, F:Y.431 Hydrogen bonds: F:D.432, F:N.449

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

SO4.2: 4 residues within 4Å: Chain A: L.226, N.229, N.230, R.317 Ligand excluded by PLIP SO4.3: 8 residues within 4Å: Chain A: D.439, K.451 Chain B: D.439, K.451 Chain C: D.439, K.451 Ligands: SO4.10, SO4.17 Ligand excluded by PLIP SO4.4: 5 residues within 4Å: Chain A: S.396, K.398, G.417, K.418, S.419 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: L.146, D.147, K.179 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain B: L.226, N.229, N.230, R.317 Ligand excluded by PLIP SO4.10: 8 residues within 4Å: Chain A: D.439, K.451 Chain B: D.439, K.451 Chain C: D.439, K.451 Ligands: SO4.3, SO4.17 Ligand excluded by PLIP SO4.11: 5 residues within 4Å: Chain B: S.396, K.398, G.417, K.418, S.419 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain B: L.146, D.147, K.179 Ligand excluded by PLIP SO4.16: 4 residues within 4Å: Chain C: L.226, N.229, N.230, R.317 Ligand excluded by PLIP SO4.17: 8 residues within 4Å: Chain A: D.439, K.451 Chain B: D.439, K.451 Chain C: D.439, K.451 Ligands: SO4.3, SO4.10 Ligand excluded by PLIP SO4.18: 5 residues within 4Å: Chain C: S.396, K.398, G.417, K.418, S.419 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain C: L.146, D.147, K.179 Ligand excluded by PLIP SO4.23: 4 residues within 4Å: Chain D: L.226, N.229, N.230, R.317 Ligand excluded by PLIP SO4.24: 8 residues within 4Å: Chain D: D.439, K.451 Chain E: D.439, K.451 Chain F: D.439, K.451 Ligands: SO4.31, SO4.38 Ligand excluded by PLIP SO4.25: 5 residues within 4Å: Chain D: S.396, K.398, G.417, K.418, S.419 Ligand excluded by PLIP SO4.26: 3 residues within 4Å: Chain D: L.146, D.147, K.179 Ligand excluded by PLIP SO4.30: 4 residues within 4Å: Chain E: L.226, N.229, N.230, R.317 Ligand excluded by PLIP SO4.31: 8 residues within 4Å: Chain D: D.439, K.451 Chain E: D.439, K.451 Chain F: D.439, K.451 Ligands: SO4.24, SO4.38 Ligand excluded by PLIP SO4.32: 5 residues within 4Å: Chain E: S.396, K.398, G.417, K.418, S.419 Ligand excluded by PLIP SO4.33: 3 residues within 4Å: Chain E: L.146, D.147, K.179 Ligand excluded by PLIP SO4.37: 4 residues within 4Å: Chain F: L.226, N.229, N.230, R.317 Ligand excluded by PLIP SO4.38: 8 residues within 4Å: Chain D: D.439, K.451 Chain E: D.439, K.451 Chain F: D.439, K.451 Ligands: SO4.24, SO4.31 Ligand excluded by PLIP SO4.39: 5 residues within 4Å: Chain F: S.396, K.398, G.417, K.418, S.419 Ligand excluded by PLIP SO4.40: 3 residues within 4Å: Chain F: L.146, D.147, K.179 Ligand excluded by PLIP

12 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 4 residues within 4Å: Chain A: Y.411 Chain C: W.27, S.99, M.323 Ligand excluded by PLIP CL.7: 7 residues within 4Å: Chain A: K.50, N.169, I.170 Chain E: K.50, N.169, I.170 Ligands: CL.35 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain A: W.27, S.99, M.323 Chain B: Y.411 Ligand excluded by PLIP CL.14: 7 residues within 4Å: Chain B: K.50, N.169, I.170 Chain D: K.50, N.169, I.170 Ligands: CL.28 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain B: W.27, S.99, M.323 Chain C: Y.411 Ligand excluded by PLIP CL.21: 7 residues within 4Å: Chain C: K.50, N.169, I.170 Chain F: K.50, N.169, I.170 Ligands: CL.42 Ligand excluded by PLIP CL.27: 4 residues within 4Å: Chain D: Y.411 Chain F: W.27, S.99, M.323 Ligand excluded by PLIP CL.28: 7 residues within 4Å: Chain B: K.50, N.169, I.170 Chain D: K.50, N.169, I.170 Ligands: CL.14 Ligand excluded by PLIP CL.34: 4 residues within 4Å: Chain D: W.27, S.99, M.323 Chain E: Y.411 Ligand excluded by PLIP CL.35: 7 residues within 4Å: Chain A: K.50, N.169, I.170 Chain E: K.50, N.169, I.170 Ligands: CL.7 Ligand excluded by PLIP CL.41: 4 residues within 4Å: Chain E: W.27, S.99, M.323 Chain F: Y.411 Ligand excluded by PLIP CL.42: 7 residues within 4Å: Chain C: K.50, N.169, I.170 Chain F: K.50, N.169, I.170 Ligands: CL.21 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Krarup, A. et al., A highly stable prefusion RSV F vaccine derived from structural analysis of the fusion mechanism. Nat Commun (2015)

Release Date

2015-09-23

Peptides

Fusion glycoprotein F0,Fibritin: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
F

C
F

D
F

E
F

F
F

Fusion glycoprotein F0,Fibritin