SMTL ID : 5jqb.1

Crystal structure of Ebola glycoprotein in complex with ibuprofen

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.68 Å

Oligo State

hetero-3-3-mer

Ligands

3 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 11 residues within 4Å: Chain A: L.43, E.129, G.130, A.131 Chain B: A.6, Q.7, P.8, N.62, T.65 Chain F: L.28 Ligands: GOL.9 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.8 NAG-NAG-BMA.12: 11 residues within 4Å: Chain B: L.28 Chain C: L.43, E.129, G.130, A.131 Chain D: A.6, Q.7, P.8, N.62, T.65 Ligands: GOL.20 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:P.8 NAG-NAG-BMA.23: 11 residues within 4Å: Chain D: L.28 Chain E: L.43, E.129, G.130, A.131 Chain F: A.6, Q.7, P.8, N.62, T.65 Ligands: GOL.31 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:P.8

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

NAG.2: 5 residues within 4Å: Chain A: T.190, L.227, N.230, E.231, Y.234 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.227 Hydrogen bonds: A:N.230 NAG.3: 2 residues within 4Å: Chain A: N.201, E.202 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.201 NAG.4: 1 residues within 4Å: Chain A: N.211 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.211 NAG.5: 4 residues within 4Å: Chain A: G.237, K.238, R.239, N.241 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.238, A:K.238 NAG.13: 5 residues within 4Å: Chain C: T.190, L.227, N.230, E.231, Y.234 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.227 Hydrogen bonds: C:N.230 NAG.14: 2 residues within 4Å: Chain C: N.201, E.202 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.201 NAG.15: 1 residues within 4Å: Chain C: N.211 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.211 NAG.16: 4 residues within 4Å: Chain C: G.237, K.238, R.239, N.241 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.238, C:K.238 NAG.24: 5 residues within 4Å: Chain E: T.190, L.227, N.230, E.231, Y.234 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:L.227 Hydrogen bonds: E:N.230 NAG.25: 2 residues within 4Å: Chain E: N.201, E.202 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.201 NAG.26: 1 residues within 4Å: Chain E: N.211 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.211 NAG.27: 4 residues within 4Å: Chain E: G.237, K.238, R.239, N.241 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.238, E:K.238

15 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 9 residues within 4Å: Chain A: N.42, L.43, E.44, T.50, R.58, N.80, Y.82, A.150, E.151 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.43, A:E.44, A:R.58, A:E.151, A:E.151 GOL.7: 5 residues within 4Å: Chain A: F.105, V.111, T.148, Y.186, S.188 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.148, A:Y.186, A:Y.186 GOL.8: 3 residues within 4Å: Chain A: E.93, C.94, D.123 No protein-ligand interaction detected (PLIP) GOL.9: 6 residues within 4Å: Chain B: N.62, E.63, T.65, Q.66 Chain F: W.30 Ligands: NAG-NAG-BMA.1 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.62, B:T.65, B:Q.66 GOL.10: 5 residues within 4Å: Chain A: F.263, W.264 Chain B: N.11, N.13, H.15 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.11 Water bridges: B:H.15, A:E.76 GOL.17: 9 residues within 4Å: Chain C: N.42, L.43, E.44, T.50, R.58, N.80, Y.82, A.150, E.151 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:L.43, C:E.44, C:R.58, C:E.151, C:E.151 GOL.18: 5 residues within 4Å: Chain C: F.105, V.111, T.148, Y.186, S.188 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.148, C:Y.186, C:Y.186 GOL.19: 3 residues within 4Å: Chain C: E.93, C.94, D.123 No protein-ligand interaction detected (PLIP) GOL.20: 6 residues within 4Å: Chain B: W.30 Chain D: N.62, E.63, T.65, Q.66 Ligands: NAG-NAG-BMA.12 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.62, D:T.65, D:Q.66 GOL.21: 5 residues within 4Å: Chain C: F.263, W.264 Chain D: N.11, N.13, H.15 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:N.11 Water bridges: D:H.15, C:E.76 GOL.28: 9 residues within 4Å: Chain E: N.42, L.43, E.44, T.50, R.58, N.80, Y.82, A.150, E.151 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:L.43, E:E.44, E:R.58, E:E.151, E:E.151 GOL.29: 5 residues within 4Å: Chain E: F.105, V.111, T.148, Y.186, S.188 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:T.148, E:Y.186, E:Y.186 GOL.30: 3 residues within 4Å: Chain E: E.93, C.94, D.123 No protein-ligand interaction detected (PLIP) GOL.31: 6 residues within 4Å: Chain D: W.30 Chain F: N.62, E.63, T.65, Q.66 Ligands: NAG-NAG-BMA.23 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:N.62, F:T.65, F:Q.66 GOL.32: 5 residues within 4Å: Chain E: F.263, W.264 Chain F: N.11, N.13, H.15 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:N.11 Water bridges: F:H.15, E:E.76

3 x IBP: IBUPROFEN(Non-covalent)

IBP.11: 8 residues within 4Å: Chain A: R.37, A.74, L.157, L.159 Chain B: L.14, Y.16, M.47, L.57 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.14, B:Y.16, B:L.57, A:L.157, A:L.159 Salt bridges: A:R.37 IBP.22: 8 residues within 4Å: Chain C: R.37, A.74, L.157, L.159 Chain D: L.14, Y.16, M.47, L.57 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:L.14, D:Y.16, D:L.57, C:L.157, C:L.159 Salt bridges: C:R.37 IBP.33: 8 residues within 4Å: Chain E: R.37, A.74, L.157, L.159 Chain F: L.14, Y.16, M.47, L.57 6 PLIP interactions: 3 interactions with chain E, 3 interactions with chain F Hydrophobic interactions: E:L.157, E:L.159, F:L.14, F:Y.16, F:L.57 Salt bridges: E:R.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, Y. et al., Toremifene interacts with and destabilizes the Ebola virus glycoprotein. Nature (2016)

Release Date

2016-06-29

Peptides

Envelope glycoprotein 1,Envelope glycoprotein 1,Envelope glycoprotein 1: ACE
Envelope glycoprotein 2: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
B

D
B

F
B

Envelope glycoprotein 1,Envelope glycoprotein 1,Envelope glycoprotein 1

Envelope glycoprotein 2

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