SMTL ID : 7ssq.1

Crystal Structure of Ebola zaire Envelope glycoprotein GP in complex with compound ARN0075231

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

hetero-3-3-mer

Ligands

3 x NAG- NAG- BMA- MAN- NAG- MAN: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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-NAG-MAN.1: 11 residues within 4Å: Chain A: L.43, E.129, G.130, A.131 Chain B: Q.7, P.8, N.62, T.65 Chain F: L.28, W.30, F.34 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.129 NAG-NAG-BMA-MAN-NAG-MAN.10: 11 residues within 4Å: Chain B: L.28, W.30, F.34 Chain C: L.43, E.129, G.130, A.131 Chain D: Q.7, P.8, N.62, T.65 1 PLIP interactions: 1 interactions with chain C Water bridges: C:E.129 NAG-NAG-BMA-MAN-NAG-MAN.19: 11 residues within 4Å: Chain D: L.28, W.30, F.34 Chain E: L.43, E.129, G.130, A.131 Chain F: Q.7, P.8, N.62, T.65 1 PLIP interactions: 1 interactions with chain E Water bridges: E:E.129

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 Hydrophobic interactions: A:L.227 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.201 NAG.11: 4 residues within 4Å: Chain C: T.190, L.227, N.230, Y.234 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.227 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: 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.14: 1 residues within 4Å: Chain C: N.201 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.201 NAG.20: 4 residues within 4Å: Chain E: T.190, L.227, N.230, Y.234 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:L.227 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: 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.23: 1 residues within 4Å: Chain E: N.201 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.201

3 x ZQH: [(4R)-4-amino-3,3-dimethylpiperidin-1-yl][(1S,3R,5R,6Z,7S)-3-phenyl-6-(2-phenylethylidene)adamantan-1-yl]methanone(Non-covalent)

ZQH.6: 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.18, M.47, L.57 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:T.18, B:L.57 Hydrogen bonds: A:R.37 ZQH.15: 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.18, M.47, L.57 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:T.18, D:L.57 Hydrogen bonds: C:R.37 ZQH.24: 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.18, M.47, L.57 14 PLIP interactions: 6 interactions with chain F, 8 interactions with chain E Hydrophobic interactions: F:L.14, F:Y.16, F:Y.16, F:Y.16, F:T.18, F:L.57, E:I.11, E:V.39, E:V.39, E:L.41, E:A.74, E:L.157, E:L.159 Hydrogen bonds: E:R.37

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

EDO.7: 4 residues within 4Å: Chain A: V.10, K.29, L.159, P.160 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.11, A:K.29, A:K.29 Water bridges: A:I.11 EDO.16: 4 residues within 4Å: Chain C: V.10, K.29, L.159, P.160 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:I.11, C:K.29, C:K.29 Water bridges: C:I.11 EDO.25: 4 residues within 4Å: Chain E: V.10, K.29, L.159, P.160 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:I.11, E:K.29, E:K.29 Water bridges: E:I.11

6 x ACT: ACETATE ION(Non-functional Binders)

ACT.8: 5 residues within 4Å: Chain A: E.93, C.94, L.95, P.96, D.123 No protein-ligand interaction detected (PLIP) ACT.9: 6 residues within 4Å: Chain A: R.103, G.104, P.106 Chain B: A.38, E.39, Y.42 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:E.39 Hydrogen bonds: B:A.38, B:Y.42 ACT.17: 5 residues within 4Å: Chain C: E.93, C.94, L.95, P.96, D.123 No protein-ligand interaction detected (PLIP) ACT.18: 6 residues within 4Å: Chain C: R.103, G.104, P.106 Chain D: A.38, E.39, Y.42 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:E.39 Hydrogen bonds: D:A.38, D:Y.42 ACT.26: 5 residues within 4Å: Chain E: E.93, C.94, L.95, P.96, D.123 No protein-ligand interaction detected (PLIP) ACT.27: 6 residues within 4Å: Chain E: R.103, G.104, P.106 Chain F: A.38, E.39, Y.42 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:E.39 Hydrogen bonds: F:A.38, F:Y.42

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 ARN0075231. to be published

Release Date

2023-08-09

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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