SMTL ID : 5jq7.1

Crystal structure of Ebola glycoprotein in complex with toremifene

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.69 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: 9 residues within 4Å: Chain A: E.129, G.130, A.131, V.153 Chain B: A.6, Q.7, P.8, N.62, T.65 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.10: 9 residues within 4Å: Chain C: E.129, G.130, A.131, V.153 Chain D: A.6, Q.7, P.8, N.62, T.65 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.19: 9 residues within 4Å: Chain E: E.129, G.130, A.131, V.153 Chain F: A.6, Q.7, P.8, N.62, T.65 No protein-ligand interaction detected (PLIP)

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:N.201 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, N.241, V.283 No protein-ligand interaction detected (PLIP) NAG.11: 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.12: 2 residues within 4Å: Chain C: N.201, E.202 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.201 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: 3 residues within 4Å: Chain C: G.237, N.241, V.283 No protein-ligand interaction detected (PLIP) NAG.20: 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.21: 2 residues within 4Å: Chain E: N.201, E.202 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.201 NAG.22: 1 residues within 4Å: Chain E: N.211 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.211 NAG.23: 3 residues within 4Å: Chain E: G.237, N.241, V.283 No protein-ligand interaction detected (PLIP)

6 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:R.145 GOL.7: 4 residues within 4Å: Chain A: N.83, E.85, K.113, G.146 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.83, A:E.85, A:E.85, A:K.113 Water bridges: A:T.148, A:T.148 GOL.15: 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:R.145 GOL.16: 4 residues within 4Å: Chain C: N.83, E.85, K.113, G.146 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.83, C:E.85, C:E.85, C:K.113 Water bridges: C:T.148, C:T.148 GOL.24: 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:R.145 GOL.25: 4 residues within 4Å: Chain E: N.83, E.85, K.113, G.146 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:N.83, E:E.85, E:E.85, E:K.113 Water bridges: E:T.148, E:T.148

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

DMS.8: 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.17: 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.26: 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

3 x T0R: Toremifene(Non-covalent)

T0R.9: 15 residues within 4Å: Chain A: R.37, V.39, L.41, E.73, A.74, G.75, L.157, L.159 Chain B: L.14, Y.16, T.18, T.19, D.21, M.47, L.57 13 PLIP interactions: 5 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:L.14, B:Y.16, B:Y.16, B:T.18, B:L.57, A:V.39, A:V.39, A:L.41, A:A.74, A:A.74, A:L.159 Hydrogen bonds: A:R.37 Salt bridges: A:E.73 T0R.18: 15 residues within 4Å: Chain C: R.37, V.39, L.41, E.73, A.74, G.75, L.157, L.159 Chain D: L.14, Y.16, T.18, T.19, D.21, M.47, L.57 13 PLIP interactions: 8 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:V.39, C:V.39, C:L.41, C:A.74, C:A.74, C:L.159, D:L.14, D:Y.16, D:Y.16, D:T.18, D:L.57 Hydrogen bonds: C:R.37 Salt bridges: C:E.73 T0R.27: 15 residues within 4Å: Chain E: R.37, V.39, L.41, E.73, A.74, G.75, L.157, L.159 Chain F: L.14, Y.16, T.18, T.19, D.21, M.47, L.57 13 PLIP interactions: 8 interactions with chain E, 5 interactions with chain F Hydrophobic interactions: E:V.39, E:V.39, E:L.41, E:A.74, E:A.74, E:L.159, F:L.14, F:Y.16, F:Y.16, F:T.18, F:L.57 Hydrogen bonds: E:R.37 Salt bridges: E:E.73

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, Y. et al., Toremifene interacts with and destabilizes the Ebola virus glycoprotein. Nature (2016)

Release Date

2016-06-29

Peptides

Envelope glycoprotein 1,Envelope glycoprotein 1,Envelope glycoprotein 1: ACE
Envelope glycoprotein 2: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
B

D
B

F
B

Envelope glycoprotein 1,Envelope glycoprotein 1,Envelope glycoprotein 1

Envelope glycoprotein 2

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