SMTL ID : 5jq3.1

Crystal structure of Ebola glycoprotein

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.23 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: 12 residues within 4Å: Chain A: L.43, K.128, E.129, G.130, A.131 Chain B: A.6, Q.7, P.8, N.62, T.65 Chain F: L.28, F.34 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.8 NAG-NAG-BMA-MAN-MAN.9: 12 residues within 4Å: Chain B: L.28, F.34 Chain C: L.43, K.128, E.129, G.130, A.131 Chain D: A.6, Q.7, P.8, N.62, T.65 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:P.8 NAG-NAG-BMA-MAN-MAN.17: 12 residues within 4Å: Chain D: L.28, F.34 Chain E: L.43, K.128, E.129, G.130, A.131 Chain F: A.6, Q.7, P.8, N.62, T.65 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:P.8

15 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 Hydrophobic interactions: A:L.227 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: 1 residues within 4Å: Chain A: N.201 No protein-ligand interaction detected (PLIP) NAG.5: 5 residues within 4Å: Chain A: G.237, K.238, R.239, N.241, V.283 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.238, A:K.238 NAG.8: 3 residues within 4Å: Chain B: N.117, K.121 Chain D: T.115 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:K.121, B:K.121 Hydrophobic interactions: D:T.115 NAG.10: 4 residues within 4Å: Chain C: T.190, L.227, N.230, Y.234 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.227 NAG.11: 1 residues within 4Å: Chain C: N.211 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.211 NAG.12: 1 residues within 4Å: Chain C: N.201 No protein-ligand interaction detected (PLIP) NAG.13: 5 residues within 4Å: Chain C: G.237, K.238, R.239, N.241, V.283 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.238, C:K.238 NAG.16: 3 residues within 4Å: Chain D: N.117, K.121 Chain F: T.115 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:K.121, D:K.121 Hydrophobic interactions: F:T.115 NAG.18: 4 residues within 4Å: Chain E: T.190, L.227, N.230, Y.234 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:L.227 NAG.19: 1 residues within 4Å: Chain E: N.211 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.211 NAG.20: 1 residues within 4Å: Chain E: N.201 No protein-ligand interaction detected (PLIP) NAG.21: 5 residues within 4Å: Chain E: G.237, K.238, R.239, N.241, V.283 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.238, E:K.238 NAG.24: 3 residues within 4Å: Chain B: T.115 Chain F: N.117, K.121 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:K.121, F:K.121 Hydrophobic interactions: B:T.115

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: W.77, E.79, F.263 Chain B: H.15 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.79, A:E.79 Water bridges: A:E.76, A:E.76, A:E.76, B:N.11 GOL.7: 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.14: 4 residues within 4Å: Chain C: W.77, E.79, F.263 Chain D: H.15 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:E.79, C:E.79 Water bridges: C:E.76, C:E.76, C:E.76, D:N.11 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:D.123 GOL.22: 4 residues within 4Å: Chain E: W.77, E.79, F.263 Chain F: H.15 6 PLIP interactions: 5 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:E.79, E:E.79 Water bridges: E:E.76, E:E.76, E:E.76, F:N.11 GOL.23: 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

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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