SMTL ID : 6f5u.1

CRYSTAL STRUCTURE OF EBOLAVIRUS GLYCOPROTEIN IN COMPLEX WITH BEPRIDIL

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 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 Chain B: A.6, Q.7, P.8, N.62, T.65 Ligands: GOL.12 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.8 NAG-NAG-BMA-MAN.15: 10 residues within 4Å: Chain C: L.43, E.129, G.130, A.131 Chain D: A.6, Q.7, P.8, N.62, T.65 Ligands: GOL.26 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:P.8 NAG-NAG-BMA-MAN.29: 10 residues within 4Å: Chain E: L.43, E.129, G.130, A.131 Chain F: A.6, Q.7, P.8, N.62, T.65 Ligands: GOL.40 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: G.237, K.238, N.241 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.238, A:K.238, 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.16: 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.17: 1 residues within 4Å: Chain C: N.211 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.211 NAG.18: 3 residues within 4Å: Chain C: G.237, K.238, N.241 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.238, C:K.238, C:N.241 NAG.19: 1 residues within 4Å: Chain C: N.201 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.201 NAG.30: 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.31: 1 residues within 4Å: Chain E: N.211 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.211 NAG.32: 3 residues within 4Å: Chain E: G.237, K.238, N.241 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:K.238, E:K.238, E:N.241 NAG.33: 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: S.63, G.64, V.65, P.66, D.123, F.124 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.64, A:V.65, A:D.123, A:D.123 Water bridges: A:V.65, A:V.65 GOL.7: 5 residues within 4Å: Chain A: E.93, C.94, L.95, P.96, D.123 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.95, A:D.123, A:R.145 GOL.8: 7 residues within 4Å: Chain A: V.10, I.11, D.28, K.29, Q.35, P.160, Q.161 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.11, A:K.29, A:Q.161 Water bridges: A:I.11 GOL.9: 3 residues within 4Å: Chain A: N.83, K.113, G.146 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.83, A:G.146, A:T.190, A:T.190 Water bridges: A:T.148 GOL.12: 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.20: 6 residues within 4Å: Chain C: S.63, G.64, V.65, P.66, D.123, F.124 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:G.64, C:V.65, C:D.123, C:D.123 Water bridges: C:V.65, C:V.65 GOL.21: 5 residues within 4Å: Chain C: E.93, C.94, L.95, P.96, D.123 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:L.95, C:D.123, C:R.145 GOL.22: 7 residues within 4Å: Chain C: V.10, I.11, D.28, K.29, Q.35, P.160, Q.161 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:I.11, C:K.29, C:Q.161 Water bridges: C:I.11 GOL.23: 3 residues within 4Å: Chain C: N.83, K.113, G.146 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.83, C:G.146, C:T.190, C:T.190 Water bridges: C:T.148 GOL.26: 6 residues within 4Å: Chain B: W.30 Chain D: N.62, E.63, T.65, Q.66 Ligands: NAG-NAG-BMA-MAN.15 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.62, D:E.63, D:T.65, D:Q.66 GOL.34: 6 residues within 4Å: Chain E: S.63, G.64, V.65, P.66, D.123, F.124 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:G.64, E:V.65, E:D.123, E:D.123 Water bridges: E:V.65, E:V.65 GOL.35: 5 residues within 4Å: Chain E: E.93, C.94, L.95, P.96, D.123 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:L.95, E:D.123, E:R.145 GOL.36: 7 residues within 4Å: Chain E: V.10, I.11, D.28, K.29, Q.35, P.160, Q.161 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:I.11, E:K.29, E:Q.161 Water bridges: E:I.11 GOL.37: 3 residues within 4Å: Chain E: N.83, K.113, G.146 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:N.83, E:G.146, E:T.190, E:T.190 Water bridges: E:T.148 GOL.40: 6 residues within 4Å: Chain D: W.30 Chain F: N.62, E.63, T.65, Q.66 Ligands: NAG-NAG-BMA-MAN.29 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:N.62, F:E.63, F:T.65, F:Q.66

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

DMS.10: 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.13: 4 residues within 4Å: Chain A: S.5, I.6 Chain B: R.86 Chain F: D.21 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.6 DMS.14: 3 residues within 4Å: Chain A: P.7 Chain B: E.1, E.63 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.1 DMS.24: 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.27: 4 residues within 4Å: Chain B: D.21 Chain C: S.5, I.6 Chain D: R.86 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:I.6 DMS.28: 3 residues within 4Å: Chain C: P.7 Chain D: E.1, E.63 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:E.1 DMS.38: 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.41: 4 residues within 4Å: Chain D: D.21 Chain E: S.5, I.6 Chain F: R.86 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:I.6 DMS.42: 3 residues within 4Å: Chain E: P.7 Chain F: E.1, E.63 1 PLIP interactions: 1 interactions with chain F Salt bridges: F:E.1

3 x CQN: Bepridil(Non-covalent)

CQN.11: 11 residues within 4Å: Chain A: R.37, V.39, A.74, G.75, L.157, L.159 Chain B: L.14, Y.16, T.18, M.47, L.57 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:L.14, B:Y.16, B:T.18, A:V.39, A:V.39, A:A.74, A:A.74, A:L.157 CQN.25: 11 residues within 4Å: Chain C: R.37, V.39, A.74, G.75, L.157, L.159 Chain D: L.14, Y.16, T.18, M.47, L.57 8 PLIP interactions: 3 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:L.14, D:Y.16, D:T.18, C:V.39, C:V.39, C:A.74, C:A.74, C:L.157 CQN.39: 11 residues within 4Å: Chain E: R.37, V.39, A.74, G.75, L.157, L.159 Chain F: L.14, Y.16, T.18, M.47, L.57 8 PLIP interactions: 3 interactions with chain F, 5 interactions with chain E Hydrophobic interactions: F:L.14, F:Y.16, F:T.18, E:V.39, E:V.39, E:A.74, E:A.74, E:L.157

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,Envelope glycoprotein,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,Envelope glycoprotein,GP1

Envelope glycoprotein

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