SMTL ID : 6f6i.1

CRYSTAL STRUCTURE OF EBOLAVIRUS GLYCOPROTEIN IN COMPLEX WITH PAROXETINE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-3-3-mer

Ligands

3 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.1: 10 residues within 4Å: Chain A: L.43, E.129, A.131, V.153 Chain B: A.6, Q.7, P.8, N.62, T.65 Ligands: GOL.11 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.8 NAG-NAG-BMA-MAN.13: 10 residues within 4Å: Chain C: L.43, E.129, A.131, V.153 Chain D: A.6, Q.7, P.8, N.62, T.65 Ligands: GOL.23 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:P.8 NAG-NAG-BMA-MAN.25: 10 residues within 4Å: Chain E: L.43, E.129, A.131, V.153 Chain F: A.6, Q.7, P.8, N.62, T.65 Ligands: GOL.35 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: 4 residues within 4Å: Chain A: T.190, L.227, N.230, Y.234 1 PLIP interactions: 1 interactions with chain A 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:E.202 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: 3 residues within 4Å: Chain A: G.237, K.238, N.241 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.241 NAG.14: 4 residues within 4Å: Chain C: T.190, L.227, N.230, Y.234 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.230 NAG.15: 2 residues within 4Å: Chain C: N.201, E.202 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.202 NAG.16: 1 residues within 4Å: Chain C: N.211 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.211 NAG.17: 3 residues within 4Å: Chain C: G.237, K.238, N.241 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.241 NAG.26: 4 residues within 4Å: Chain E: T.190, L.227, N.230, Y.234 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.230 NAG.27: 2 residues within 4Å: Chain E: N.201, E.202 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.202 NAG.28: 1 residues within 4Å: Chain E: N.211 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.211 NAG.29: 3 residues within 4Å: Chain E: G.237, K.238, N.241 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.241

3 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.6: 5 residues within 4Å: Chain A: E.93, C.94, L.95, P.96, D.123 No protein-ligand interaction detected (PLIP) DMS.18: 5 residues within 4Å: Chain C: E.93, C.94, L.95, P.96, D.123 No protein-ligand interaction detected (PLIP) DMS.30: 5 residues within 4Å: Chain E: E.93, C.94, L.95, P.96, D.123 No protein-ligand interaction detected (PLIP)

15 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 7 residues within 4Å: Chain A: S.63, G.64, V.65, P.66, P.67, D.123, F.124 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.64, A:D.123, A:D.123 Water bridges: A:V.65 GOL.8: 7 residues within 4Å: Chain A: G.104, F.105, P.106, V.111, T.148, Y.186, S.188 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.105, A:Y.186, A:S.188 Water bridges: A:P.106 GOL.9: 8 residues within 4Å: Chain A: V.10, I.11, D.28, K.29, I.158, L.159, P.160, Q.161 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.11, A:D.28, A:K.29, A:Q.161, A:Q.161 GOL.11: 6 residues within 4Å: Chain B: N.62, E.63, T.65, Q.66 Chain F: W.30 Ligands: NAG-NAG-BMA-MAN.1 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.62, B:E.63, B:T.65, B:Q.66 GOL.12: 4 residues within 4Å: Chain B: N.11, N.13, H.15, L.46 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.11 Water bridges: B:N.13, B:H.15 GOL.19: 7 residues within 4Å: Chain C: S.63, G.64, V.65, P.66, P.67, D.123, F.124 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.64, C:D.123, C:D.123 Water bridges: C:V.65 GOL.20: 7 residues within 4Å: Chain C: G.104, F.105, P.106, V.111, T.148, Y.186, S.188 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:F.105, C:Y.186, C:S.188 Water bridges: C:P.106 GOL.21: 8 residues within 4Å: Chain C: V.10, I.11, D.28, K.29, I.158, L.159, P.160, Q.161 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:I.11, C:D.28, C:K.29, C:Q.161, C:Q.161 GOL.23: 6 residues within 4Å: Chain B: W.30 Chain D: N.62, E.63, T.65, Q.66 Ligands: NAG-NAG-BMA-MAN.13 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.62, D:E.63, D:T.65, D:Q.66 GOL.24: 4 residues within 4Å: Chain D: N.11, N.13, H.15, L.46 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.11 Water bridges: D:N.13, D:H.15 GOL.31: 7 residues within 4Å: Chain E: S.63, G.64, V.65, P.66, P.67, D.123, F.124 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:G.64, E:D.123, E:D.123 Water bridges: E:V.65 GOL.32: 7 residues within 4Å: Chain E: G.104, F.105, P.106, V.111, T.148, Y.186, S.188 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:F.105, E:Y.186, E:S.188 Water bridges: E:P.106 GOL.33: 8 residues within 4Å: Chain E: V.10, I.11, D.28, K.29, I.158, L.159, P.160, Q.161 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:I.11, E:D.28, E:K.29, E:Q.161, E:Q.161 GOL.35: 6 residues within 4Å: Chain D: W.30 Chain F: N.62, E.63, T.65, Q.66 Ligands: NAG-NAG-BMA-MAN.25 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:N.62, F:E.63, F:T.65, F:Q.66 GOL.36: 4 residues within 4Å: Chain F: N.11, N.13, H.15, L.46 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:N.11 Water bridges: F:N.13, F:H.15

3 x 8PR: Paroxetine(Non-covalent)

8PR.10: 13 residues within 4Å: Chain A: R.37, V.39, G.40, L.41, E.73, A.74, G.75, L.159 Chain B: L.14, Y.16, T.18, M.47, L.57 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.14, B:Y.16, B:L.57, A:R.37, A:V.39, A:A.74 Water bridges: B:Y.16 pi-Cation interactions: A:R.37 8PR.22: 13 residues within 4Å: Chain C: R.37, V.39, G.40, L.41, E.73, A.74, G.75, L.159 Chain D: L.14, Y.16, T.18, M.47, L.57 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:R.37, C:V.39, C:A.74, D:L.14, D:Y.16, D:L.57 pi-Cation interactions: C:R.37 Water bridges: D:Y.16 8PR.34: 13 residues within 4Å: Chain E: R.37, V.39, G.40, L.41, E.73, A.74, G.75, L.159 Chain F: L.14, Y.16, T.18, M.47, L.57 8 PLIP interactions: 4 interactions with chain E, 4 interactions with chain F Hydrophobic interactions: E:R.37, E:V.39, E:A.74, F:L.14, F:Y.16, F:L.57 pi-Cation interactions: E:R.37 Water bridges: F:Y.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ren, J. et al., Target Identification and Mode of Action of Four Chemically Divergent Drugs against Ebolavirus Infection. J. Med. Chem. (2018)

Release Date

2018-01-03

Peptides

Envelope glycoprotein,GP,GP1: ACE
Envelope glycoprotein: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
B

D
B

F
B

Envelope glycoprotein,GP,GP1

Envelope glycoprotein

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