SMTL ID : 6g9b.1

Crystal structure of Ebolavirus glycoprotein in complex with imipramine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.26 Å

Oligo State

hetero-3-3-mer

Ligands

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 9 residues within 4Å: Chain A: L.43, E.129, G.130, A.131 Chain B: Q.7, P.8, N.62, T.65 Ligands: GOL.13 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 9 residues within 4Å: Chain C: L.43, E.129, G.130, A.131 Chain D: Q.7, P.8, N.62, T.65 Ligands: GOL.29 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 9 residues within 4Å: Chain E: L.43, E.129, G.130, A.131 Chain F: Q.7, P.8, N.62, T.65 Ligands: GOL.45 No protein-ligand interaction detected (PLIP)

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

NAG.2: 6 residues within 4Å: Chain A: T.189, T.190, L.227, N.230, E.231, 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: 2 residues within 4Å: Chain A: N.201, E.202 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.202 NAG.5: 3 residues within 4Å: Chain A: K.238, R.239, N.241 No protein-ligand interaction detected (PLIP) NAG.18: 6 residues within 4Å: Chain C: T.189, T.190, L.227, N.230, E.231, Y.234 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.230 NAG.19: 1 residues within 4Å: Chain C: N.211 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.211 NAG.20: 2 residues within 4Å: Chain C: N.201, E.202 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.202 NAG.21: 3 residues within 4Å: Chain C: K.238, R.239, N.241 No protein-ligand interaction detected (PLIP) NAG.34: 6 residues within 4Å: Chain E: T.189, T.190, L.227, N.230, E.231, Y.234 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.230 NAG.35: 1 residues within 4Å: Chain E: N.211 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.211 NAG.36: 2 residues within 4Å: Chain E: N.201, E.202 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.202 NAG.37: 3 residues within 4Å: Chain E: K.238, R.239, N.241 No protein-ligand interaction detected (PLIP)

18 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: W.77, A.78, E.79, F.263 Chain B: H.15 Ligand excluded by PLIP GOL.7: 7 residues within 4Å: Chain A: E.93, C.94, L.95, P.96, D.123, F.124, R.145 Ligand excluded by PLIP GOL.8: 8 residues within 4Å: Chain A: V.10, I.11, D.28, K.29, Q.35, L.159, P.160, Q.161 Ligand excluded by PLIP GOL.9: 9 residues within 4Å: Chain A: N.42, L.43, E.44, T.50, R.58, N.80, Y.82, A.150, E.151 Ligand excluded by PLIP GOL.13: 6 residues within 4Å: Chain B: N.62, E.63, T.65, Q.66 Chain F: W.30 Ligands: NAG-NAG.1 Ligand excluded by PLIP GOL.14: 9 residues within 4Å: Chain A: S.5, D.20, V.21, D.22 Chain B: K.87, D.90 Chain E: S.32, N.34 Ligands: DMS.11 Ligand excluded by PLIP GOL.22: 5 residues within 4Å: Chain C: W.77, A.78, E.79, F.263 Chain D: H.15 Ligand excluded by PLIP GOL.23: 7 residues within 4Å: Chain C: E.93, C.94, L.95, P.96, D.123, F.124, R.145 Ligand excluded by PLIP GOL.24: 8 residues within 4Å: Chain C: V.10, I.11, D.28, K.29, Q.35, L.159, P.160, Q.161 Ligand excluded by PLIP GOL.25: 9 residues within 4Å: Chain C: N.42, L.43, E.44, T.50, R.58, N.80, Y.82, A.150, E.151 Ligand excluded by PLIP GOL.29: 6 residues within 4Å: Chain B: W.30 Chain D: N.62, E.63, T.65, Q.66 Ligands: NAG-NAG.17 Ligand excluded by PLIP GOL.30: 9 residues within 4Å: Chain A: S.32, N.34 Chain C: S.5, D.20, V.21, D.22 Chain D: K.87, D.90 Ligands: DMS.27 Ligand excluded by PLIP GOL.38: 5 residues within 4Å: Chain E: W.77, A.78, E.79, F.263 Chain F: H.15 Ligand excluded by PLIP GOL.39: 7 residues within 4Å: Chain E: E.93, C.94, L.95, P.96, D.123, F.124, R.145 Ligand excluded by PLIP GOL.40: 8 residues within 4Å: Chain E: V.10, I.11, D.28, K.29, Q.35, L.159, P.160, Q.161 Ligand excluded by PLIP GOL.41: 9 residues within 4Å: Chain E: N.42, L.43, E.44, T.50, R.58, N.80, Y.82, A.150, E.151 Ligand excluded by PLIP GOL.45: 6 residues within 4Å: Chain D: W.30 Chain F: N.62, E.63, T.65, Q.66 Ligands: NAG-NAG.33 Ligand excluded by PLIP GOL.46: 9 residues within 4Å: Chain C: S.32, N.34 Chain E: S.5, D.20, V.21, D.22 Chain F: K.87, D.90 Ligands: DMS.43 Ligand excluded by PLIP

6 x IXX: 3-(5H-DIBENZO[B,F]AZEPIN-5-YL)-N,N-DIMETHYLPROPAN-1-AMINE(Non-covalent)

IXX.10: 9 residues within 4Å: Chain A: I.11, L.16, V.39, L.157, I.158, L.159 Chain B: L.14, M.47 Ligands: IXX.15 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.11, A:I.11, A:L.16, A:V.39, A:L.157, A:L.157, B:L.14 IXX.15: 6 residues within 4Å: Chain A: R.37, A.74 Chain B: Y.16, Q.20, I.43 Ligands: IXX.10 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.16, A:A.74 Hydrogen bonds: B:Q.20 IXX.26: 9 residues within 4Å: Chain C: I.11, L.16, V.39, L.157, I.158, L.159 Chain D: L.14, M.47 Ligands: IXX.31 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:I.11, C:I.11, C:L.16, C:V.39, C:L.157, C:L.157, D:L.14 IXX.31: 6 residues within 4Å: Chain C: R.37, A.74 Chain D: Y.16, Q.20, I.43 Ligands: IXX.26 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:Y.16, C:A.74 Hydrogen bonds: D:Q.20 IXX.42: 9 residues within 4Å: Chain E: I.11, L.16, V.39, L.157, I.158, L.159 Chain F: L.14, M.47 Ligands: IXX.47 7 PLIP interactions: 6 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:I.11, E:I.11, E:L.16, E:V.39, E:L.157, E:L.157, F:L.14 IXX.47: 6 residues within 4Å: Chain E: R.37, A.74 Chain F: Y.16, Q.20, I.43 Ligands: IXX.42 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: E:A.74, F:Y.16 Hydrogen bonds: F:Q.20

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

DMS.11: 7 residues within 4Å: Chain A: R.4, S.5, I.6 Chain B: F.71, R.86, K.87 Ligands: GOL.14 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.87, A:I.6 DMS.12: 3 residues within 4Å: Chain A: Y.186, Y.187, S.188 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.188 DMS.16: 6 residues within 4Å: Chain A: V.18 Chain B: E.1, A.2, I.3, V.4, E.63 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.4 Salt bridges: B:E.1, B:E.63 DMS.27: 7 residues within 4Å: Chain C: R.4, S.5, I.6 Chain D: F.71, R.86, K.87 Ligands: GOL.30 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:I.6, D:K.87 DMS.28: 3 residues within 4Å: Chain C: Y.186, Y.187, S.188 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.188 DMS.32: 6 residues within 4Å: Chain C: V.18 Chain D: E.1, A.2, I.3, V.4, E.63 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:V.4 Salt bridges: D:E.1, D:E.63 DMS.43: 7 residues within 4Å: Chain E: R.4, S.5, I.6 Chain F: F.71, R.86, K.87 Ligands: GOL.46 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:I.6, F:K.87 DMS.44: 3 residues within 4Å: Chain E: Y.186, Y.187, S.188 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.188 DMS.48: 6 residues within 4Å: Chain E: V.18 Chain F: E.1, A.2, I.3, V.4, E.63 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:V.4 Salt bridges: F:E.1, F:E.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, Y. et al., Structures of Ebola Virus Glycoprotein Complexes with Tricyclic Antidepressant and Antipsychotic Drugs. J. Med. Chem. (2018)

Release Date

2018-05-23

Peptides

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

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