SMTL ID : 6nae.1

Crystal Structure of Ebola zaire GP protein with bound ARN0074898

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

hetero-3-3-mer

Ligands

3 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[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-MAN.1: 11 residues within 4Å: Chain A: L.43, K.128, E.129, G.130, A.131, V.153 Chain B: 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-MAN.12: 11 residues within 4Å: Chain C: L.43, K.128, E.129, G.130, A.131, V.153 Chain D: Q.7, P.8, N.62, T.65 Ligands: GOL.22 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:P.8 NAG-NAG-BMA-MAN-MAN.23: 11 residues within 4Å: Chain E: L.43, K.128, E.129, G.130, A.131, V.153 Chain F: Q.7, P.8, N.62, T.65 Ligands: GOL.33 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: 1 residues within 4Å: Chain A: N.211 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.211 NAG.4: 3 residues within 4Å: Chain A: S.236, G.237, N.241 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.241 NAG.5: 1 residues within 4Å: Chain A: N.201 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.201 NAG.13: 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.14: 1 residues within 4Å: Chain C: N.211 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.211 NAG.15: 3 residues within 4Å: Chain C: S.236, G.237, N.241 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.241 NAG.16: 1 residues within 4Å: Chain C: N.201 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.201 NAG.24: 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.25: 1 residues within 4Å: Chain E: N.211 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.211 NAG.26: 3 residues within 4Å: Chain E: S.236, G.237, N.241 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.241 NAG.27: 1 residues within 4Å: Chain E: N.201 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.201

15 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain A: E.93, C.94, L.95, P.96, D.123, R.145 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.123, A:R.145 Water bridges: A:A.97 GOL.7: 5 residues within 4Å: Chain A: G.47, V.48, A.49, T.50, D.51 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.50, A:T.50, A:D.51, A:D.51, A:D.51 GOL.8: 6 residues within 4Å: Chain A: R.220, F.221, T.222, F.225, P.252, E.253 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.220, A:T.222, A:P.252 GOL.10: 3 residues within 4Å: Chain A: S.19, V.21 Chain B: Q.94 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:K.87, A:S.5, A:S.19, A:S.19 Water bridges: B:Q.94 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-MAN.1 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.62, B:N.62, B:E.63, B:T.65, B:Q.66 GOL.17: 6 residues within 4Å: Chain C: E.93, C.94, L.95, P.96, D.123, R.145 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.123, C:R.145 Water bridges: C:A.97 GOL.18: 5 residues within 4Å: Chain C: G.47, V.48, A.49, T.50, D.51 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.50, C:T.50, C:D.51, C:D.51, C:D.51 GOL.19: 6 residues within 4Å: Chain C: R.220, F.221, T.222, F.225, P.252, E.253 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.220, C:T.222, C:P.252 GOL.21: 3 residues within 4Å: Chain C: S.19, V.21 Chain D: Q.94 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:K.87, C:S.5, C:S.19, C:S.19 Water bridges: D:Q.94 GOL.22: 6 residues within 4Å: Chain B: W.30 Chain D: N.62, E.63, T.65, Q.66 Ligands: NAG-NAG-BMA-MAN-MAN.12 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:N.62, D:N.62, D:E.63, D:T.65, D:Q.66 GOL.28: 6 residues within 4Å: Chain E: E.93, C.94, L.95, P.96, D.123, R.145 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:D.123, E:R.145 Water bridges: E:A.97 GOL.29: 5 residues within 4Å: Chain E: G.47, V.48, A.49, T.50, D.51 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:T.50, E:T.50, E:D.51, E:D.51, E:D.51 GOL.30: 6 residues within 4Å: Chain E: R.220, F.221, T.222, F.225, P.252, E.253 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.220, E:T.222, E:P.252 GOL.32: 3 residues within 4Å: Chain E: S.19, V.21 Chain F: Q.94 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:S.5, E:S.19, E:S.19, F:K.87 Water bridges: F:Q.94 GOL.33: 6 residues within 4Å: Chain D: W.30 Chain F: N.62, E.63, T.65, Q.66 Ligands: NAG-NAG-BMA-MAN-MAN.23 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:N.62, F:N.62, F:E.63, F:T.65, F:Q.66

3 x KHG: (1S,3R,5R,7S)-N-(trans-4-aminocyclohexyl)-3-methyl-5-phenyltricyclo[3.3.1.1~3,7~]decane-1-carboxamide(Non-covalent)

KHG.9: 10 residues within 4Å: Chain A: R.37, V.39, G.40, L.41, A.74, G.75, L.159 Chain B: L.14, Y.16, M.47 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:V.39, A:V.39, A:L.41, A:A.74, B:L.14, B:Y.16, B:Y.16, B:Y.16 Hydrogen bonds: A:R.37 KHG.20: 10 residues within 4Å: Chain C: R.37, V.39, G.40, L.41, A.74, G.75, L.159 Chain D: L.14, Y.16, M.47 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:V.39, C:V.39, C:L.41, C:A.74, D:L.14, D:Y.16, D:Y.16, D:Y.16 Hydrogen bonds: C:R.37 KHG.31: 10 residues within 4Å: Chain E: R.37, V.39, G.40, L.41, A.74, G.75, L.159 Chain F: L.14, Y.16, M.47 9 PLIP interactions: 5 interactions with chain E, 4 interactions with chain F Hydrophobic interactions: E:V.39, E:V.39, E:L.41, E:A.74, F:L.14, F:Y.16, F:Y.16, F:Y.16 Hydrogen bonds: E:R.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Plewe, M.B. et al., Discovery of Adamantane Carboxamides as Ebola Virus Cell Entry and Glycoprotein Inhibitors. Acs Med.Chem.Lett. (2020)

Release Date

2019-12-11

Peptides

Envelope glycoprotein,Envelope glycoprotein,Envelope glycoprotein: 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,Envelope glycoprotein,Envelope glycoprotein

Envelope glycoprotein

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