SMTL ID : 5c69.1

Crystal Structure of Prefusion-stabilized RSV F variant PR-DM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-hexamer

Ligands

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

SO4.1: 2 residues within 4Å: Chain A: F.85, R.287 Ligand excluded by PLIP SO4.2: 5 residues within 4Å: Chain A: S.391, K.393, G.412, K.413, S.414 Ligand excluded by PLIP SO4.3: 4 residues within 4Å: Chain A: L.221, N.224, N.225, R.312 Ligand excluded by PLIP SO4.4: 4 residues within 4Å: Chain A: V.140, L.141, D.142, K.174 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: E.184, V.187, N.188 Ligand excluded by PLIP SO4.6: 4 residues within 4Å: Chain A: N.392, K.393, G.394, K.409 Ligand excluded by PLIP SO4.7: 3 residues within 4Å: Chain A: N.374, N.376, R.377 Ligand excluded by PLIP SO4.15: 2 residues within 4Å: Chain B: F.85, R.287 Ligand excluded by PLIP SO4.16: 5 residues within 4Å: Chain B: S.391, K.393, G.412, K.413, S.414 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain B: L.221, N.224, N.225, R.312 Ligand excluded by PLIP SO4.18: 4 residues within 4Å: Chain B: V.140, L.141, D.142, K.174 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain B: E.184, V.187, N.188 Ligand excluded by PLIP SO4.20: 4 residues within 4Å: Chain B: N.392, K.393, G.394, K.409 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain B: N.374, N.376, R.377 Ligand excluded by PLIP SO4.29: 2 residues within 4Å: Chain C: F.85, R.287 Ligand excluded by PLIP SO4.30: 5 residues within 4Å: Chain C: S.391, K.393, G.412, K.413, S.414 Ligand excluded by PLIP SO4.31: 4 residues within 4Å: Chain C: L.221, N.224, N.225, R.312 Ligand excluded by PLIP SO4.32: 4 residues within 4Å: Chain C: V.140, L.141, D.142, K.174 Ligand excluded by PLIP SO4.33: 3 residues within 4Å: Chain C: E.184, V.187, N.188 Ligand excluded by PLIP SO4.34: 4 residues within 4Å: Chain C: N.392, K.393, G.394, K.409 Ligand excluded by PLIP SO4.35: 3 residues within 4Å: Chain C: N.374, N.376, R.377 Ligand excluded by PLIP SO4.43: 2 residues within 4Å: Chain D: F.85, R.287 Ligand excluded by PLIP SO4.44: 5 residues within 4Å: Chain D: S.391, K.393, G.412, K.413, S.414 Ligand excluded by PLIP SO4.45: 4 residues within 4Å: Chain D: L.221, N.224, N.225, R.312 Ligand excluded by PLIP SO4.46: 4 residues within 4Å: Chain D: V.140, L.141, D.142, K.174 Ligand excluded by PLIP SO4.47: 3 residues within 4Å: Chain D: E.184, V.187, N.188 Ligand excluded by PLIP SO4.48: 4 residues within 4Å: Chain D: N.392, K.393, G.394, K.409 Ligand excluded by PLIP SO4.49: 3 residues within 4Å: Chain D: N.374, N.376, R.377 Ligand excluded by PLIP SO4.57: 2 residues within 4Å: Chain E: F.85, R.287 Ligand excluded by PLIP SO4.58: 5 residues within 4Å: Chain E: S.391, K.393, G.412, K.413, S.414 Ligand excluded by PLIP SO4.59: 4 residues within 4Å: Chain E: L.221, N.224, N.225, R.312 Ligand excluded by PLIP SO4.60: 4 residues within 4Å: Chain E: V.140, L.141, D.142, K.174 Ligand excluded by PLIP SO4.61: 3 residues within 4Å: Chain E: E.184, V.187, N.188 Ligand excluded by PLIP SO4.62: 4 residues within 4Å: Chain E: N.392, K.393, G.394, K.409 Ligand excluded by PLIP SO4.63: 3 residues within 4Å: Chain E: N.374, N.376, R.377 Ligand excluded by PLIP SO4.71: 2 residues within 4Å: Chain F: F.85, R.287 Ligand excluded by PLIP SO4.72: 5 residues within 4Å: Chain F: S.391, K.393, G.412, K.413, S.414 Ligand excluded by PLIP SO4.73: 4 residues within 4Å: Chain F: L.221, N.224, N.225, R.312 Ligand excluded by PLIP SO4.74: 4 residues within 4Å: Chain F: V.140, L.141, D.142, K.174 Ligand excluded by PLIP SO4.75: 3 residues within 4Å: Chain F: E.184, V.187, N.188 Ligand excluded by PLIP SO4.76: 4 residues within 4Å: Chain F: N.392, K.393, G.394, K.409 Ligand excluded by PLIP SO4.77: 3 residues within 4Å: Chain F: N.374, N.376, R.377 Ligand excluded by PLIP

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

NHE.8: 8 residues within 4Å: Chain A: F.85, L.86, G.87, F.88, Q.302 Chain C: F.88 Ligands: NHE.22, NHE.36 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:F.85, A:F.85, A:G.87, A:F.88, A:Q.302 Hydrophobic interactions: C:F.88, C:F.88 NHE.9: 7 residues within 4Å: Chain A: F.335, F.425, Y.426, D.427, V.430, N.444, I.447 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.335, A:F.425, A:Y.426 Hydrogen bonds: A:D.427, A:N.444 NHE.22: 8 residues within 4Å: Chain A: F.88 Chain B: F.85, L.86, G.87, F.88, Q.302 Ligands: NHE.8, NHE.36 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:F.85, B:G.87, B:F.88, B:Q.302 Hydrophobic interactions: A:F.88, A:F.88 NHE.23: 7 residues within 4Å: Chain B: F.335, F.425, Y.426, D.427, V.430, N.444, I.447 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.335, B:F.425, B:Y.426 Hydrogen bonds: B:D.427, B:N.444 NHE.36: 8 residues within 4Å: Chain B: F.88 Chain C: F.85, L.86, G.87, F.88, Q.302 Ligands: NHE.8, NHE.22 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:F.85, C:F.85, C:G.87, C:F.88, C:Q.302 Hydrophobic interactions: B:F.88, B:F.88 NHE.37: 7 residues within 4Å: Chain C: F.335, F.425, Y.426, D.427, V.430, N.444, I.447 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.335, C:F.425, C:Y.426 Hydrogen bonds: C:D.427, C:N.444 NHE.50: 8 residues within 4Å: Chain D: F.85, L.86, G.87, F.88, Q.302 Chain F: F.88 Ligands: NHE.64, NHE.78 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain F Hydrogen bonds: D:F.85, D:G.87, D:F.88, D:Q.302 Hydrophobic interactions: F:F.88, F:F.88 NHE.51: 7 residues within 4Å: Chain D: F.335, F.425, Y.426, D.427, V.430, N.444, I.447 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.335, D:F.425, D:Y.426 Hydrogen bonds: D:D.427, D:N.444 NHE.64: 8 residues within 4Å: Chain D: F.88 Chain E: F.85, L.86, G.87, F.88, Q.302 Ligands: NHE.50, NHE.78 7 PLIP interactions: 5 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:F.85, E:F.85, E:G.87, E:F.88, E:Q.302 Hydrophobic interactions: D:F.88, D:F.88 NHE.65: 7 residues within 4Å: Chain E: F.335, F.425, Y.426, D.427, V.430, N.444, I.447 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:F.335, E:F.425, E:Y.426 Hydrogen bonds: E:D.427, E:N.444 NHE.78: 8 residues within 4Å: Chain E: F.88 Chain F: F.85, L.86, G.87, F.88, Q.302 Ligands: NHE.50, NHE.64 6 PLIP interactions: 4 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:F.85, F:G.87, F:F.88, F:Q.302 Hydrophobic interactions: E:F.88, E:F.88 NHE.79: 7 residues within 4Å: Chain F: F.335, F.425, Y.426, D.427, V.430, N.444, I.447 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:F.335, F:F.425, F:Y.426 Hydrogen bonds: F:D.427, F:N.444

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

CL.10: 5 residues within 4Å: Chain A: N.164, I.165 Chain E: N.164, I.165 Ligands: CL.66 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: W.27, S.94 Chain B: Y.406 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain A: K.263, W.289, A.303 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain A: Q.410, E.411 Chain C: K.104 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain A: P.432, S.450 Ligand excluded by PLIP CL.24: 5 residues within 4Å: Chain B: N.164, I.165 Chain D: N.164, I.165 Ligands: CL.52 Ligand excluded by PLIP CL.25: 3 residues within 4Å: Chain B: W.27, S.94 Chain C: Y.406 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain B: K.263, W.289, A.303 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain A: K.104 Chain B: Q.410, E.411 Ligand excluded by PLIP CL.28: 2 residues within 4Å: Chain B: P.432, S.450 Ligand excluded by PLIP CL.38: 5 residues within 4Å: Chain C: N.164, I.165 Chain F: N.164, I.165 Ligands: CL.80 Ligand excluded by PLIP CL.39: 3 residues within 4Å: Chain A: Y.406 Chain C: W.27, S.94 Ligand excluded by PLIP CL.40: 3 residues within 4Å: Chain C: K.263, W.289, A.303 Ligand excluded by PLIP CL.41: 3 residues within 4Å: Chain B: K.104 Chain C: Q.410, E.411 Ligand excluded by PLIP CL.42: 2 residues within 4Å: Chain C: P.432, S.450 Ligand excluded by PLIP CL.52: 5 residues within 4Å: Chain B: N.164, I.165 Chain D: N.164, I.165 Ligands: CL.24 Ligand excluded by PLIP CL.53: 3 residues within 4Å: Chain D: W.27, S.94 Chain E: Y.406 Ligand excluded by PLIP CL.54: 3 residues within 4Å: Chain D: K.263, W.289, A.303 Ligand excluded by PLIP CL.55: 3 residues within 4Å: Chain D: Q.410, E.411 Chain F: K.104 Ligand excluded by PLIP CL.56: 2 residues within 4Å: Chain D: P.432, S.450 Ligand excluded by PLIP CL.66: 5 residues within 4Å: Chain A: N.164, I.165 Chain E: N.164, I.165 Ligands: CL.10 Ligand excluded by PLIP CL.67: 3 residues within 4Å: Chain E: W.27, S.94 Chain F: Y.406 Ligand excluded by PLIP CL.68: 3 residues within 4Å: Chain E: K.263, W.289, A.303 Ligand excluded by PLIP CL.69: 3 residues within 4Å: Chain D: K.104 Chain E: Q.410, E.411 Ligand excluded by PLIP CL.70: 2 residues within 4Å: Chain E: P.432, S.450 Ligand excluded by PLIP CL.80: 5 residues within 4Å: Chain C: N.164, I.165 Chain F: N.164, I.165 Ligands: CL.38 Ligand excluded by PLIP CL.81: 3 residues within 4Å: Chain D: Y.406 Chain F: W.27, S.94 Ligand excluded by PLIP CL.82: 3 residues within 4Å: Chain F: K.263, W.289, A.303 Ligand excluded by PLIP CL.83: 3 residues within 4Å: Chain E: K.104 Chain F: Q.410, E.411 Ligand excluded by PLIP CL.84: 2 residues within 4Å: Chain F: P.432, S.450 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
A

B
A

C
A

D
A

E
A

F
A

Fusion glycoprotein F0,Fibritin