SMTL ID : 6g9i.1

Crystal structure of Ebolavirus glycoprotein in complex with clomipramine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.19 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, G.130, A.131, V.153 Chain B: Q.7, P.8, N.62, T.65 Ligands: GOL.8 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.8 NAG-NAG-BMA-MAN.11: 10 residues within 4Å: Chain C: L.43, E.129, G.130, A.131, V.153 Chain D: Q.7, P.8, N.62, T.65 Ligands: GOL.18 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:P.8 NAG-NAG-BMA-MAN.21: 10 residues within 4Å: Chain E: L.43, E.129, G.130, A.131, V.153 Chain F: Q.7, P.8, N.62, T.65 Ligands: GOL.28 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.230 Water bridges: A:N.230, A:E.231 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: 4 residues within 4Å: Chain A: G.237, R.239, N.241, V.283 No protein-ligand interaction detected (PLIP) NAG.12: 4 residues within 4Å: Chain C: T.190, L.227, N.230, Y.234 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.230 Water bridges: C:N.230, C:E.231 NAG.13: 1 residues within 4Å: Chain C: N.211 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.211 NAG.14: 2 residues within 4Å: Chain C: N.201, E.202 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.202 NAG.15: 4 residues within 4Å: Chain C: G.237, R.239, N.241, V.283 No protein-ligand interaction detected (PLIP) NAG.22: 4 residues within 4Å: Chain E: T.190, L.227, N.230, Y.234 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.230 Water bridges: E:N.230, E:E.231 NAG.23: 1 residues within 4Å: Chain E: N.211 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.211 NAG.24: 2 residues within 4Å: Chain E: N.201, E.202 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.202 NAG.25: 4 residues within 4Å: Chain E: G.237, R.239, N.241, V.283 No protein-ligand interaction detected (PLIP)

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: E.93, C.94, L.95, P.96, D.123 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.95, A:D.123 GOL.7: 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:E.44, A:R.58, A:N.80, A:E.151, A:E.151 GOL.8: 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.9: 7 residues within 4Å: Chain B: E.77, S.82 Chain F: F.81, S.82, N.85 Ligands: GOL.19, GOL.29 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain F Hydrogen bonds: B:E.77, B:S.82, F:N.85 Water bridges: F:E.77, F:F.81 GOL.16: 5 residues within 4Å: Chain C: E.93, C.94, L.95, P.96, D.123 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.95, C:D.123 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:E.44, C:R.58, C:N.80, C:E.151, C:E.151 GOL.18: 6 residues within 4Å: Chain B: W.30 Chain D: N.62, E.63, T.65, Q.66 Ligands: NAG-NAG-BMA-MAN.11 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.62, D:E.63, D:T.65, D:Q.66 GOL.19: 7 residues within 4Å: Chain B: F.81, S.82, N.85 Chain D: E.77, S.82 Ligands: GOL.9, GOL.29 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:N.85, D:E.77, D:S.82 Water bridges: B:E.77, B:F.81 GOL.26: 5 residues within 4Å: Chain E: E.93, C.94, L.95, P.96, D.123 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:L.95, E:D.123 GOL.27: 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:E.44, E:R.58, E:N.80, E:E.151, E:E.151 GOL.28: 6 residues within 4Å: Chain D: W.30 Chain F: N.62, E.63, T.65, Q.66 Ligands: NAG-NAG-BMA-MAN.21 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:N.62, F:E.63, F:T.65, F:Q.66 GOL.29: 7 residues within 4Å: Chain D: F.81, S.82, N.85 Chain F: E.77, S.82 Ligands: GOL.9, GOL.19 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain F Hydrogen bonds: D:N.85, F:E.77, F:S.82 Water bridges: D:E.77, D:F.81

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

CXX.10: 7 residues within 4Å: Chain A: I.11, L.16, V.39, L.157, L.159 Chain B: M.47, L.57 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.11, A:L.16, A:V.39, A:L.157, B:L.57 CXX.20: 7 residues within 4Å: Chain C: I.11, L.16, V.39, L.157, L.159 Chain D: M.47, L.57 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:I.11, C:L.16, C:V.39, C:L.157, D:L.57 CXX.30: 7 residues within 4Å: Chain E: I.11, L.16, V.39, L.157, L.159 Chain F: M.47, L.57 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:I.11, E:L.16, E:V.39, E:L.157, F:L.57

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,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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