SMTL ID : 3cl5.1

Structure of coronavirus hemagglutinin-esterase in complex with 4,9-O-diacetyl sialic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 9 residues within 4Å: Chain A: K.169, S.203, Y.205, N.218, N.246, E.247 Chain B: F.207, I.214, I.244 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 9 residues within 4Å: Chain A: F.207, I.214, I.244 Chain B: K.169, S.203, Y.205, N.218, N.246, E.247 No protein-ligand interaction detected (PLIP)

10 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 3 residues within 4Å: Chain A: N.283, A.286, V.287 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.283 NAG.3: 5 residues within 4Å: Chain A: N.71, T.73, T.126, F.127, N.129 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.73, A:T.126, A:F.127, A:N.129 NAG.4: 4 residues within 4Å: Chain A: F.1, Y.338, N.340 Chain B: D.358 No protein-ligand interaction detected (PLIP) NAG.5: 8 residues within 4Å: Chain A: D.272, R.274, N.283, A.286, F.296, N.298, S.299, T.300 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:N.283, A:A.286, A:F.296 Hydrogen bonds: A:D.272, A:R.274, A:N.298, A:T.300 NAG.6: 5 residues within 4Å: Chain A: P.34, N.36, S.38, V.306, Y.307 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.36, A:S.38, A:V.306 NAG.11: 3 residues within 4Å: Chain B: N.283, A.286, V.287 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.283 NAG.12: 5 residues within 4Å: Chain B: N.71, T.73, T.126, F.127, N.129 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.127, B:N.129 NAG.13: 4 residues within 4Å: Chain A: D.358 Chain B: F.1, Y.338, N.340 No protein-ligand interaction detected (PLIP) NAG.14: 8 residues within 4Å: Chain B: D.272, R.274, N.283, A.286, F.296, N.298, S.299, T.300 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:N.283, B:A.286, B:F.296 Hydrogen bonds: B:D.272, B:R.274, B:N.298, B:T.300 NAG.15: 5 residues within 4Å: Chain B: P.34, N.36, S.38, V.306, Y.307 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.36, B:S.38, B:V.306

2 x SIO: methyl 4,9-di-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid(Non-covalent)

SIO.7: 7 residues within 4Å: Chain A: Y.166, F.193, L.194, S.195, N.196, L.248, L.249 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.166, A:F.193, A:F.193, A:L.194, A:L.248, A:L.249 Hydrogen bonds: A:L.194, A:S.195, A:N.196 Water bridges: A:S.98, A:S.195, A:T.197 SIO.16: 7 residues within 4Å: Chain B: Y.166, F.193, L.194, S.195, N.196, L.248, L.249 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.166, B:F.193, B:F.193, B:L.194, B:L.248, B:L.249 Hydrogen bonds: B:L.194, B:S.195, B:N.196 Water bridges: B:S.98, B:Y.166, B:T.197

2 x K: POTASSIUM ION(Non-covalent)

K.8: 6 residues within 4Å: Chain A: D.202, S.203, Q.204, S.245, E.247, L.249 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.202, A:S.203, A:S.245, A:E.247, A:L.249 K.17: 6 residues within 4Å: Chain B: D.202, S.203, Q.204, S.245, E.247, L.249 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.202, B:S.203, B:S.245, B:E.247, B:L.249

2 x ACY: ACETIC ACID(Non-functional Binders)

ACY.9: 7 residues within 4Å: Chain A: D.21, A.22, R.23, A.56, G.57, N.86, H.311 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.22 Hydrogen bonds: A:A.22, A:G.57, A:N.86 Salt bridges: A:H.311 ACY.18: 7 residues within 4Å: Chain B: D.21, A.22, R.23, A.56, G.57, N.86, H.311 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:A.22 Hydrogen bonds: B:A.22, B:G.57, B:N.86 Salt bridges: B:H.311

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Zeng, Q. et al., Structure of coronavirus hemagglutinin-esterase offers insight into corona and influenza virus evolution. Proc.Natl.Acad.Sci.Usa (2008)

Release Date

2008-06-03

Peptides

Hemagglutinin-esterase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Hemagglutinin-esterase