SMTL ID : 7lyy.1

Crystal Structure of Ebola zaire Envelope glycoprotein GP in complex with compound ARN0075164

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 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: Q.7, P.8, N.62, T.65 Ligands: EDO.9 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.8 NAG-NAG-BMA-MAN.10: 9 residues within 4Å: Chain C: E.129, G.130, A.131, V.153 Chain D: Q.7, P.8, N.62, T.65 Ligands: EDO.18 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:P.8 NAG-NAG-BMA-MAN.19: 9 residues within 4Å: Chain E: E.129, G.130, A.131, V.153 Chain F: Q.7, P.8, N.62, T.65 Ligands: EDO.27 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: 3 residues within 4Å: Chain A: T.190, 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, R.239, N.241 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.241 NAG.5: 1 residues within 4Å: Chain A: N.201 No protein-ligand interaction detected (PLIP) NAG.11: 3 residues within 4Å: Chain C: T.190, N.230, Y.234 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.230 NAG.12: 1 residues within 4Å: Chain C: N.211 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.211 NAG.13: 3 residues within 4Å: Chain C: G.237, R.239, N.241 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.241 NAG.14: 1 residues within 4Å: Chain C: N.201 No protein-ligand interaction detected (PLIP) NAG.20: 3 residues within 4Å: Chain E: T.190, N.230, Y.234 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.230 NAG.21: 1 residues within 4Å: Chain E: N.211 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.211 NAG.22: 3 residues within 4Å: Chain E: G.237, R.239, N.241 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.241 NAG.23: 1 residues within 4Å: Chain E: N.201 No protein-ligand interaction detected (PLIP)

9 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 4 residues within 4Å: Chain A: E.93, C.94, L.95, D.123 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.123 EDO.7: 4 residues within 4Å: Chain A: S.19, D.20, V.21 Chain B: Q.94 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.20, B:K.87 EDO.9: 6 residues within 4Å: Chain B: N.62, E.63, T.65, Q.66 Chain F: W.30 Ligands: NAG-NAG-BMA-MAN.1 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.62, B:E.63, B:Q.66 EDO.15: 4 residues within 4Å: Chain C: E.93, C.94, L.95, D.123 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.123 EDO.16: 4 residues within 4Å: Chain C: S.19, D.20, V.21 Chain D: Q.94 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:D.20, D:K.87 EDO.18: 6 residues within 4Å: Chain B: W.30 Chain D: N.62, E.63, T.65, Q.66 Ligands: NAG-NAG-BMA-MAN.10 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.62, D:E.63, D:Q.66 EDO.24: 4 residues within 4Å: Chain E: E.93, C.94, L.95, D.123 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.123 EDO.25: 4 residues within 4Å: Chain E: S.19, D.20, V.21 Chain F: Q.94 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:D.20, F:K.87 EDO.27: 6 residues within 4Å: Chain D: W.30 Chain F: N.62, E.63, T.65, Q.66 Ligands: NAG-NAG-BMA-MAN.19 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:N.62, F:E.63, F:Q.66

3 x YPM: (1s,3R,5S,7s)-N-[(1r,4r)-4-aminocyclohexyl]-3,5-diphenyladamantane-1-carboxamide(Non-covalent)

YPM.8: 14 residues within 4Å: Chain A: I.11, R.37, V.39, G.40, L.41, A.74, G.75, L.157, L.159 Chain B: L.14, Y.16, T.19, M.47, L.53 14 PLIP interactions: 8 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:I.11, A:V.39, A:V.39, A:L.41, A:A.74, A:L.157, A:L.159, B:L.14, B:Y.16, B:Y.16, B:Y.16, B:Y.16, B:L.53 Hydrogen bonds: A:R.37 YPM.17: 14 residues within 4Å: Chain C: I.11, R.37, V.39, G.40, L.41, A.74, G.75, L.157, L.159 Chain D: L.14, Y.16, T.19, M.47, L.53 14 PLIP interactions: 8 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:I.11, C:V.39, C:V.39, C:L.41, C:A.74, C:L.157, C:L.159, D:L.14, D:Y.16, D:Y.16, D:Y.16, D:Y.16, D:L.53 Hydrogen bonds: C:R.37 YPM.26: 14 residues within 4Å: Chain E: I.11, R.37, V.39, G.40, L.41, A.74, G.75, L.157, L.159 Chain F: L.14, Y.16, T.19, M.47, L.53 14 PLIP interactions: 8 interactions with chain E, 6 interactions with chain F Hydrophobic interactions: E:I.11, E:V.39, E:V.39, E:L.41, E:A.74, E:L.157, E:L.159, F:L.14, F:Y.16, F:Y.16, F:Y.16, F:Y.16, F:L.53 Hydrogen bonds: E:R.37

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 ARN0075164. 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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