SMTL ID : 7ssr.1

Crystal Structure of Ebola zaire Envelope glycoprotein GP in complex with compound ARN0075093

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 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 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:K.128 Hydrophobic interactions: B:P.8 NAG-NAG-BMA-MAN.10: 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 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:P.8 Water bridges: C:K.128 NAG-NAG-BMA-MAN.19: 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 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:P.8 Water bridges: E:K.128

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 No protein-ligand interaction detected (PLIP) 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 No protein-ligand interaction detected (PLIP) NAG.5: 1 residues within 4Å: Chain A: N.201 No protein-ligand interaction detected (PLIP) NAG.11: 4 residues within 4Å: Chain C: T.190, L.227, N.230, Y.234 No protein-ligand interaction detected (PLIP) 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 No protein-ligand interaction detected (PLIP) NAG.14: 1 residues within 4Å: Chain C: N.201 No protein-ligand interaction detected (PLIP) NAG.20: 4 residues within 4Å: Chain E: T.190, L.227, N.230, Y.234 No protein-ligand interaction detected (PLIP) 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 No protein-ligand interaction detected (PLIP) NAG.23: 1 residues within 4Å: Chain E: N.201 No protein-ligand interaction detected (PLIP)

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

EDO.6: 5 residues within 4Å: Chain A: V.10, I.11, D.28, K.29, P.160 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:I.11, A:K.29, A:K.29, A:Q.35, A:Q.161 Water bridges: A:I.11 EDO.15: 5 residues within 4Å: Chain C: V.10, I.11, D.28, K.29, P.160 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:I.11, C:K.29, C:K.29, C:Q.35, C:Q.161 Water bridges: C:I.11 EDO.24: 5 residues within 4Å: Chain E: V.10, I.11, D.28, K.29, P.160 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:I.11, E:K.29, E:K.29, E:Q.35, E:Q.161 Water bridges: E:I.11

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

ACT.7: 5 residues within 4Å: Chain A: E.93, C.94, L.95, P.96, D.123 No protein-ligand interaction detected (PLIP) ACT.8: 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.16: 5 residues within 4Å: Chain C: E.93, C.94, L.95, P.96, D.123 No protein-ligand interaction detected (PLIP) ACT.17: 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.25: 5 residues within 4Å: Chain E: E.93, C.94, L.95, P.96, D.123 No protein-ligand interaction detected (PLIP) ACT.26: 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

3 x ZTL: (1R,2s,3S,5s,7s)-N-[(1r,4r)-4-(aminomethyl)cyclohexyl]-5-phenyladamantane-2-carboxamide(Non-covalent)

ZTL.9: 12 residues within 4Å: Chain A: R.37, V.39, A.74, L.157 Chain B: L.14, Y.16, Q.20, D.21, I.43, M.47, L.53, L.57 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.14, B:Y.16, B:Y.16, B:I.43, B:L.53, B:L.57, A:V.39, A:L.157, A:L.157 Hydrogen bonds: B:Q.20, B:D.21, B:D.21, A:R.37 ZTL.18: 12 residues within 4Å: Chain C: R.37, V.39, A.74, L.157 Chain D: L.14, Y.16, Q.20, D.21, I.43, M.47, L.53, L.57 13 PLIP interactions: 4 interactions with chain C, 9 interactions with chain D Hydrophobic interactions: C:V.39, C:L.157, C:L.157, D:L.14, D:Y.16, D:Y.16, D:I.43, D:L.53, D:L.57 Hydrogen bonds: C:R.37, D:Q.20, D:D.21, D:D.21 ZTL.27: 12 residues within 4Å: Chain E: R.37, V.39, A.74, L.157 Chain F: L.14, Y.16, Q.20, D.21, I.43, M.47, L.53, L.57 13 PLIP interactions: 4 interactions with chain E, 9 interactions with chain F Hydrophobic interactions: E:V.39, E:L.157, E:L.157, F:L.14, F:Y.16, F:Y.16, F:I.43, F:L.53, F:L.57 Hydrogen bonds: E:R.37, F:Q.20, F:D.21, F:D.21

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 ARN0075093. 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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