SMTL ID : 7m2d.1

Crystal Structure of Ebola zaire Envelope glycoprotein GP in complex with compound ARN0074953

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 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: L.43, E.129, G.130, A.131, V.153 Chain B: Q.7, P.8, N.62, T.65 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.8 NAG-NAG-BMA-MAN.7: 9 residues within 4Å: Chain C: L.43, E.129, G.130, A.131, V.153 Chain D: 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.13: 9 residues within 4Å: Chain E: L.43, E.129, G.130, A.131, V.153 Chain F: Q.7, P.8, N.62, T.65 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 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: 4 residues within 4Å: Chain A: G.237, R.239, N.241, L.246 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.8: 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.9: 1 residues within 4Å: Chain C: N.211 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.211 NAG.10: 4 residues within 4Å: Chain C: G.237, R.239, N.241, L.246 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.241 NAG.11: 1 residues within 4Å: Chain C: N.201 No protein-ligand interaction detected (PLIP) NAG.14: 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.15: 1 residues within 4Å: Chain E: N.211 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.211 NAG.16: 4 residues within 4Å: Chain E: G.237, R.239, N.241, L.246 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.241 NAG.17: 1 residues within 4Å: Chain E: N.201 No protein-ligand interaction detected (PLIP)

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

YPS.6: 12 residues within 4Å: Chain A: R.37, V.39, G.40, A.74, G.75, L.159 Chain B: L.14, Y.16, T.18, T.19, M.47, L.57 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.14, B:Y.16, B:Y.16, B:Y.16, B:Y.16, B:T.18, B:L.57, A:V.39, A:V.39, A:A.74 Hydrogen bonds: A:R.37 YPS.12: 12 residues within 4Å: Chain C: R.37, V.39, G.40, A.74, G.75, L.159 Chain D: L.14, Y.16, T.18, T.19, M.47, L.57 11 PLIP interactions: 4 interactions with chain C, 7 interactions with chain D Hydrophobic interactions: C:V.39, C:V.39, C:A.74, D:L.14, D:Y.16, D:Y.16, D:Y.16, D:Y.16, D:T.18, D:L.57 Hydrogen bonds: C:R.37 YPS.18: 12 residues within 4Å: Chain E: R.37, V.39, G.40, A.74, G.75, L.159 Chain F: L.14, Y.16, T.18, T.19, M.47, L.57 11 PLIP interactions: 4 interactions with chain E, 7 interactions with chain F Hydrophobic interactions: E:V.39, E:V.39, E:A.74, F:L.14, F:Y.16, F:Y.16, F:Y.16, F:Y.16, F:T.18, F:L.57 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 ARN0074953. 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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