SMTL ID : 6eam.1

CRYSTAL STRUCTURE OF HUMAN RESPIRATORY SYNCYTIAL VIRUS FUSION GLYCOPROTEIN INHIBITOR ESCAPE VARIANT E487D STABILIZED IN THE PREFUSION STATE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.74 Å

Oligo State

homo-trimer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: N.496, N.500 Ligands: NHE.3 No protein-ligand interaction detected (PLIP) NAG.12: 3 residues within 4Å: Chain B: N.496, N.500 Ligands: NHE.14 No protein-ligand interaction detected (PLIP) NAG.23: 3 residues within 4Å: Chain C: N.496, N.500 Ligands: NHE.25 No protein-ligand interaction detected (PLIP)

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

NHE.2: 9 residues within 4Å: Chain A: F.137, G.139, F.140, Q.354, F.488 Chain C: F.140 Ligands: SO4.4, NHE.13, NHE.24 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:F.137, A:F.140, A:F.488, C:F.140, C:F.140 Hydrogen bonds: A:G.139, A:F.140, A:Q.354 NHE.3: 9 residues within 4Å: Chain A: F.387, F.477, Y.478, D.479, V.482, N.496, I.499, L.503 Ligands: NAG.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.387, A:F.477, A:Y.478 Hydrogen bonds: A:D.479 NHE.13: 9 residues within 4Å: Chain A: F.140 Chain B: F.137, G.139, F.140, Q.354, F.488 Ligands: NHE.2, SO4.15, NHE.24 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.137, B:F.140, B:F.488, A:F.140, A:F.140 Hydrogen bonds: B:G.139, B:F.140, B:Q.354 NHE.14: 9 residues within 4Å: Chain B: F.387, F.477, Y.478, D.479, V.482, N.496, I.499, L.503 Ligands: NAG.12 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.387, B:F.477, B:Y.478 Hydrogen bonds: B:D.479 NHE.24: 9 residues within 4Å: Chain B: F.140 Chain C: F.137, G.139, F.140, Q.354, F.488 Ligands: NHE.2, NHE.13, SO4.26 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:F.137, C:F.140, C:F.488, B:F.140, B:F.140 Hydrogen bonds: C:G.139, C:F.140, C:Q.354 NHE.25: 9 residues within 4Å: Chain C: F.387, F.477, Y.478, D.479, V.482, N.496, I.499, L.503 Ligands: NAG.23 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.387, C:F.477, C:Y.478 Hydrogen bonds: C:D.479

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

SO4.4: 6 residues within 4Å: Chain A: F.137, R.339, Q.354, E.356 Chain C: R.106 Ligands: NHE.2 Ligand excluded by PLIP SO4.5: 4 residues within 4Å: Chain A: L.273, N.276, N.277, R.364 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain A: L.193, D.194, K.226 Ligand excluded by PLIP SO4.7: 8 residues within 4Å: Chain A: R.49, W.52, S.146, A.147, M.370 Chain B: L.456, Y.457, Y.458 Ligand excluded by PLIP SO4.8: 4 residues within 4Å: Chain A: N.426, N.428, R.429 Ligands: SO4.9 Ligand excluded by PLIP SO4.9: 5 residues within 4Å: Chain A: N.444, K.445, G.446, K.461 Ligands: SO4.8 Ligand excluded by PLIP SO4.10: 2 residues within 4Å: Chain A: G.471, E.472 Ligand excluded by PLIP SO4.15: 6 residues within 4Å: Chain A: R.106 Chain B: F.137, R.339, Q.354, E.356 Ligands: NHE.13 Ligand excluded by PLIP SO4.16: 4 residues within 4Å: Chain B: L.273, N.276, N.277, R.364 Ligand excluded by PLIP SO4.17: 3 residues within 4Å: Chain B: L.193, D.194, K.226 Ligand excluded by PLIP SO4.18: 8 residues within 4Å: Chain B: R.49, W.52, S.146, A.147, M.370 Chain C: L.456, Y.457, Y.458 Ligand excluded by PLIP SO4.19: 4 residues within 4Å: Chain B: N.426, N.428, R.429 Ligands: SO4.20 Ligand excluded by PLIP SO4.20: 5 residues within 4Å: Chain B: N.444, K.445, G.446, K.461 Ligands: SO4.19 Ligand excluded by PLIP SO4.21: 2 residues within 4Å: Chain B: G.471, E.472 Ligand excluded by PLIP SO4.26: 6 residues within 4Å: Chain B: R.106 Chain C: F.137, R.339, Q.354, E.356 Ligands: NHE.24 Ligand excluded by PLIP SO4.27: 4 residues within 4Å: Chain C: L.273, N.276, N.277, R.364 Ligand excluded by PLIP SO4.28: 3 residues within 4Å: Chain C: L.193, D.194, K.226 Ligand excluded by PLIP SO4.29: 8 residues within 4Å: Chain A: L.456, Y.457, Y.458 Chain C: R.49, W.52, S.146, A.147, M.370 Ligand excluded by PLIP SO4.30: 4 residues within 4Å: Chain C: N.426, N.428, R.429 Ligands: SO4.31 Ligand excluded by PLIP SO4.31: 5 residues within 4Å: Chain C: N.444, K.445, G.446, K.461 Ligands: SO4.30 Ligand excluded by PLIP SO4.32: 2 residues within 4Å: Chain C: G.471, E.472 Ligand excluded by PLIP

3 x TAR: D(-)-TARTARIC ACID(Non-covalent)

TAR.11: 5 residues within 4Å: Chain A: S.443, K.445, G.464, K.465, S.466 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.443, A:S.466 TAR.22: 5 residues within 4Å: Chain B: S.443, K.445, G.464, K.465, S.466 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.443, B:S.466 TAR.33: 5 residues within 4Å: Chain C: S.443, K.445, G.464, K.465, S.466 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.443, C:S.466

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Battles, M.B. et al., Structural Basis for Respiratory Syncytial Virus Fusion Inhibitor Resistance. To be published

Release Date

2019-08-07

Peptides

Fusion glycoprotein F0: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
F

C
F

Fusion glycoprotein F0