SMTL ID : 7lyd.1

Crystal Structure of Ebola zaire Envelope glycoprotein GP in complex with compound ARN0075146

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 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: 11 residues within 4Å: Chain A: L.43, K.128, E.129, G.130, A.131, V.153 Chain B: Q.7, P.8, N.62, T.65 Ligands: GOL.8 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:E.129 Hydrophobic interactions: B:P.8 NAG-NAG-BMA-MAN-MAN.9: 11 residues within 4Å: Chain C: L.43, K.128, E.129, G.130, A.131, V.153 Chain D: Q.7, P.8, N.62, T.65 Ligands: GOL.16 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Water bridges: C:E.129 Hydrophobic interactions: D:P.8 NAG-NAG-BMA-MAN-MAN.17: 11 residues within 4Å: Chain E: L.43, K.128, E.129, G.130, A.131, V.153 Chain F: Q.7, P.8, N.62, T.65 Ligands: GOL.24 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F Water bridges: E:E.129 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.230 Water bridges: 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: 6 residues within 4Å: Chain A: G.237, K.238, R.239, N.241, L.246, W.248 No protein-ligand interaction detected (PLIP) NAG.5: 1 residues within 4Å: Chain A: N.201 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.201 NAG.10: 4 residues within 4Å: Chain C: T.190, L.227, N.230, Y.234 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.230 Water bridges: C:N.230 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: 6 residues within 4Å: Chain C: G.237, K.238, R.239, N.241, L.246, W.248 No protein-ligand interaction detected (PLIP) NAG.13: 1 residues within 4Å: Chain C: N.201 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.201 NAG.18: 4 residues within 4Å: Chain E: T.190, L.227, N.230, Y.234 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.230 Water bridges: E:N.230 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: 6 residues within 4Å: Chain E: G.237, K.238, R.239, N.241, L.246, W.248 No protein-ligand interaction detected (PLIP) NAG.21: 1 residues within 4Å: Chain E: N.201 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.201

3 x YOD: (1R,3S,5S,7S)-N-[(1r,4R)-4-aminocyclohexyl]-3-[(methylsulfanyl)methyl]-5-phenyladamantane-1-carboxamide(Non-covalent)

YOD.6: 10 residues within 4Å: Chain A: R.37, V.39, G.40, A.74, G.75, L.159 Chain B: L.14, Y.16, T.19, M.47 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:V.39, A:V.39, A:L.159, A:L.159, B:L.14, B:Y.16, B:Y.16, B:Y.16, B:Y.16 Hydrogen bonds: A:R.37 YOD.14: 10 residues within 4Å: Chain C: R.37, V.39, G.40, A.74, G.75, L.159 Chain D: L.14, Y.16, T.19, M.47 10 PLIP interactions: 5 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:L.14, D:Y.16, D:Y.16, D:Y.16, D:Y.16, C:V.39, C:V.39, C:L.159, C:L.159 Hydrogen bonds: C:R.37 YOD.22: 10 residues within 4Å: Chain E: R.37, V.39, G.40, A.74, G.75, L.159 Chain F: L.14, Y.16, T.19, M.47 10 PLIP interactions: 5 interactions with chain E, 5 interactions with chain F Hydrophobic interactions: E:V.39, E:V.39, E:L.159, E:L.159, F:L.14, F:Y.16, F:Y.16, F:Y.16, F:Y.16 Hydrogen bonds: E:R.37

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: E.93, C.94, L.95, P.96, D.123, R.145 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.123, A:D.123, A:R.145 Water bridges: A:A.97 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-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.15: 6 residues within 4Å: Chain C: E.93, C.94, L.95, P.96, D.123, R.145 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.123, C:D.123, C:R.145 Water bridges: C:A.97 GOL.16: 6 residues within 4Å: Chain B: W.30 Chain D: N.62, E.63, T.65, Q.66 Ligands: NAG-NAG-BMA-MAN-MAN.9 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.62, D:E.63, D:T.65, D:Q.66 GOL.23: 6 residues within 4Å: Chain E: E.93, C.94, L.95, P.96, D.123, R.145 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:D.123, E:D.123, E:R.145 Water bridges: E:A.97 GOL.24: 6 residues within 4Å: Chain D: W.30 Chain F: N.62, E.63, T.65, Q.66 Ligands: NAG-NAG-BMA-MAN-MAN.17 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:N.62, F:E.63, F:T.65, F:Q.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abendroth, J. et al., Crystal Structure of Ebola zaire Envelope glycoprotein GP in complex with compound ARN0075146. to be published

Release Date

2021-11-24

Peptides

GP1: ACE
GP2: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
B

D
B

F
B

GP1

GP2

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