SMTL ID : 6f6n.1

CRYSTAL STRUCTURE OF EBOLAVIRUS GLYCOPROTEIN IN COMPLEX WITH SERTRALINE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 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: 10 residues within 4Å: Chain A: L.43, E.129, A.131 Chain B: Q.7, P.8, N.62, T.65 Chain F: L.28, F.34 Ligands: GOL.11 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.8 NAG-NAG-BMA-MAN-MAN.13: 10 residues within 4Å: Chain B: L.28, F.34 Chain C: L.43, E.129, A.131 Chain D: Q.7, P.8, N.62, T.65 Ligands: GOL.23 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:P.8 NAG-NAG-BMA-MAN-MAN.25: 10 residues within 4Å: Chain D: L.28, F.34 Chain E: L.43, E.129, A.131 Chain F: Q.7, P.8, N.62, T.65 Ligands: GOL.35 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 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.227 Hydrogen bonds: A:N.230 Water bridges: A:N.230, A:E.231 NAG.3: 2 residues within 4Å: Chain A: N.201, E.202 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.202, A:E.202 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: 5 residues within 4Å: Chain A: G.237, K.238, R.239, N.241, L.246 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.238, A:K.238 NAG.14: 4 residues within 4Å: Chain C: T.190, L.227, N.230, Y.234 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.227 Hydrogen bonds: C:N.230 Water bridges: C:N.230, C:E.231 NAG.15: 2 residues within 4Å: Chain C: N.201, E.202 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.202, C:E.202 NAG.16: 1 residues within 4Å: Chain C: N.211 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.211 NAG.17: 5 residues within 4Å: Chain C: G.237, K.238, R.239, N.241, L.246 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.238, C:K.238 NAG.26: 4 residues within 4Å: Chain E: T.190, L.227, N.230, Y.234 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:L.227 Hydrogen bonds: E:N.230 Water bridges: E:N.230, E:E.231 NAG.27: 2 residues within 4Å: Chain E: N.201, E.202 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:E.202, E:E.202 NAG.28: 1 residues within 4Å: Chain E: N.211 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.211 NAG.29: 5 residues within 4Å: Chain E: G.237, K.238, R.239, N.241, L.246 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.238, E:K.238

15 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain A: T.33, L.36, E.73 Chain B: L.84, N.85 Chain D: R.86 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:L.36 Water bridges: A:N.71, B:F.81 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.44, A:R.58, A:E.151, A:E.151 GOL.8: 5 residues within 4Å: Chain A: E.93, C.94, L.95, P.96, D.123 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.93, A:D.123, A:R.145 Water bridges: A:A.97 GOL.11: 6 residues within 4Å: Chain B: N.62, E.63, T.65, Q.66 Chain F: W.30 Ligands: NAG-NAG-BMA-MAN-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.12: 7 residues within 4Å: Chain A: A.15, L.16 Chain B: I.3, D.51, G.52, L.53, G.56 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:L.16, B:I.3, B:D.51 GOL.18: 6 residues within 4Å: Chain C: T.33, L.36, E.73 Chain D: L.84, N.85 Chain F: R.86 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Water bridges: D:F.81, C:N.71 Hydrogen bonds: C:L.36 GOL.19: 9 residues within 4Å: Chain C: N.42, L.43, E.44, T.50, R.58, N.80, Y.82, A.150, E.151 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.44, C:R.58, C:E.151, C:E.151 GOL.20: 5 residues within 4Å: Chain C: E.93, C.94, L.95, P.96, D.123 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.93, C:D.123, C:R.145 Water bridges: C:A.97 GOL.23: 6 residues within 4Å: Chain B: W.30 Chain D: N.62, E.63, T.65, Q.66 Ligands: NAG-NAG-BMA-MAN-MAN.13 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.62, D:E.63, D:T.65, D:Q.66 GOL.24: 7 residues within 4Å: Chain C: A.15, L.16 Chain D: I.3, D.51, G.52, L.53, G.56 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:I.3, D:D.51, C:L.16 GOL.30: 6 residues within 4Å: Chain B: R.86 Chain E: T.33, L.36, E.73 Chain F: L.84, N.85 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:L.36 Water bridges: E:N.71, F:F.81 GOL.31: 9 residues within 4Å: Chain E: N.42, L.43, E.44, T.50, R.58, N.80, Y.82, A.150, E.151 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:E.44, E:R.58, E:E.151, E:E.151 GOL.32: 5 residues within 4Å: Chain E: E.93, C.94, L.95, P.96, D.123 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:E.93, E:D.123, E:R.145 Water bridges: E:A.97 GOL.35: 6 residues within 4Å: Chain D: W.30 Chain F: N.62, E.63, T.65, Q.66 Ligands: NAG-NAG-BMA-MAN-MAN.25 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:N.62, F:E.63, F:T.65, F:Q.66 GOL.36: 7 residues within 4Å: Chain E: A.15, L.16 Chain F: I.3, D.51, G.52, L.53, G.56 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:L.16, F:I.3, F:D.51

3 x SRE: (1S,4S)-4-(3,4-dichlorophenyl)-N-methyl-1,2,3,4-tetrahydronaphthalen-1-amine(Non-covalent)

SRE.9: 10 residues within 4Å: Chain A: I.11, R.37, V.39, A.74, L.157, L.159 Chain B: Y.16, M.47, L.53, L.57 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Y.16, A:R.37, A:V.39, A:A.74, A:L.159 Halogen bonds: B:L.53 SRE.21: 10 residues within 4Å: Chain C: I.11, R.37, V.39, A.74, L.157, L.159 Chain D: Y.16, M.47, L.53, L.57 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:Y.16, C:R.37, C:V.39, C:A.74, C:L.159 Halogen bonds: D:L.53 SRE.33: 10 residues within 4Å: Chain E: I.11, R.37, V.39, A.74, L.157, L.159 Chain F: Y.16, M.47, L.53, L.57 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: E:R.37, E:V.39, E:A.74, E:L.159, F:Y.16 Halogen bonds: F:L.53

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

DMS.10: 6 residues within 4Å: Chain A: F.263, W.264 Chain B: N.11, N.13, H.15, L.46 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.11 Water bridges: B:N.13, B:H.15 DMS.22: 6 residues within 4Å: Chain C: F.263, W.264 Chain D: N.11, N.13, H.15, L.46 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.11 Water bridges: D:N.13, D:H.15 DMS.34: 6 residues within 4Å: Chain E: F.263, W.264 Chain F: N.11, N.13, H.15, L.46 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:N.11 Water bridges: F:N.13, F:H.15

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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