SMTL ID : 6sg8.1

Structure of Sosuga virus receptor binding protein

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

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

NAG.1: 1 residues within 4Å: Chain A: N.331 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.331 NAG.2: 6 residues within 4Å: Chain A: P.276, D.278, N.279, E.326, S.327, V.328 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.328 Hydrogen bonds: A:D.278 NAG.3: 3 residues within 4Å: Chain A: H.54, N.77, D.78 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.77, A:D.78 NAG.4: 1 residues within 4Å: Chain A: N.141 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.141 Water bridges: A:N.141 NAG.10: 2 residues within 4Å: Chain B: N.331, D.401 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.401, B:D.401 Water bridges: B:N.331, B:N.331 NAG.11: 6 residues within 4Å: Chain B: P.276, D.278, N.279, E.326, S.327, K.371 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:P.276, B:D.278 Hydrogen bonds: B:N.279, B:E.326, B:S.327, B:K.371 NAG.12: 4 residues within 4Å: Chain B: H.54, N.77, D.78 Ligands: ACT.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.77, B:D.78 NAG.13: 3 residues within 4Å: Chain B: N.141, T.143, Q.144 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.143 NAG.14: 6 residues within 4Å: Chain B: L.291, N.292, I.364, R.365, K.366, L.368 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.291 Hydrogen bonds: B:K.366, B:L.368, B:D.376 NAG.15: 2 residues within 4Å: Chain B: F.206, N.216 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.216

10 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 4 residues within 4Å: Chain A: R.58, F.415, E.447, M.448 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.447 Salt bridges: A:R.58 ACT.6: 6 residues within 4Å: Chain A: S.76, N.77, P.85, V.87, Q.115 Chain B: K.41 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.115 Salt bridges: B:K.41 ACT.7: 5 residues within 4Å: Chain A: H.121, E.142, Y.183, H.201, E.285 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.183 Hydrogen bonds: A:E.285 Salt bridges: A:H.121, A:H.201 ACT.8: 4 residues within 4Å: Chain A: E.39 Chain B: N.77 Ligands: NAG.12, ACT.16 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.39 ACT.16: 7 residues within 4Å: Chain A: K.41 Chain B: V.75, S.76, N.77, P.85, Q.115 Ligands: ACT.8 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.77, B:Q.115 Salt bridges: A:K.41 ACT.17: 5 residues within 4Å: Chain B: R.58, F.415, E.447, M.448 Ligands: ACT.20 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.58 ACT.18: 5 residues within 4Å: Chain B: H.121, E.142, Y.183, H.201, E.285 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.121 ACT.19: 2 residues within 4Å: Chain B: L.95, T.97 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.97 ACT.20: 4 residues within 4Å: Chain B: D.441, E.447, M.448 Ligands: ACT.17 No protein-ligand interaction detected (PLIP) ACT.21: 6 residues within 4Å: Chain A: R.44 Chain B: R.44, D.45, F.46, H.105, T.107 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Salt bridges: A:R.44 Hydrophobic interactions: B:R.44 Hydrogen bonds: B:H.105, B:T.107, B:T.107

2 x CA: CALCIUM ION(Non-covalent)

CA.9: 4 residues within 4Å: Chain A: D.145, T.148, G.150, Y.180 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.145, A:D.145, A:T.148, A:T.148, A:G.150 CA.22: 4 residues within 4Å: Chain B: D.145, T.148, G.150, Y.180 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.145, B:D.145, B:T.148, B:T.148, B:G.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stelfox, A.J. et al., A structure-based rationale for sialic acid independent host-cell entry of Sosuga virus. Proc.Natl.Acad.Sci.USA (2019)

Release Date

2019-10-09

Peptides

Hemagglutinin-neuraminidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Hemagglutinin-neuraminidase