SMTL ID : 5jil.1

Crystal structure of rat coronavirus strain New-Jersey Hemagglutinin-Esterase in complex with 4N-acetyl sialic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 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: 7 residues within 4Å: Chain A: V.170, S.209, N.224, L.257, E.258 Chain B: Y.213, K.253 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.170 NAG-NAG.13: 7 residues within 4Å: Chain A: Y.213, K.253 Chain B: V.170, S.209, N.224, L.257, E.258 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.170

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

NAG.2: 3 residues within 4Å: Chain A: A.134, N.174, T.215 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.174 NAG.3: 8 residues within 4Å: Chain A: N.287, S.288, T.289, D.313, Y.314, S.315, G.316, V.321 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.289 Hydrogen bonds: A:D.313, A:G.316 NAG.4: 3 residues within 4Å: Chain A: N.294, A.297, V.298 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.294 NAG.5: 9 residues within 4Å: Chain A: D.283, R.285, N.294, A.297, F.307, N.309, T.310, S.311, A.312 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:N.294, A:A.297, A:F.307 Hydrogen bonds: A:D.283, A:S.311 Water bridges: A:N.309, A:N.309 NAG.6: 5 residues within 4Å: Chain A: N.14, D.15, L.336, Y.337, N.338 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.15 Water bridges: A:N.338, A:N.338 NAG.7: 4 residues within 4Å: Chain A: Y.350, N.352, V.353 Chain B: I.371 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.353 Hydrogen bonds: A:N.352 NAG.8: 4 residues within 4Å: Chain A: F.70, N.72, I.128, T.130 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.70 Hydrogen bonds: A:N.72, A:I.128 Water bridges: A:T.130 NAG.14: 3 residues within 4Å: Chain B: A.134, N.174, T.215 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.174 NAG.15: 8 residues within 4Å: Chain B: N.287, S.288, T.289, D.313, Y.314, S.315, G.316, V.321 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.289 Hydrogen bonds: B:D.313, B:G.316 NAG.16: 3 residues within 4Å: Chain B: N.294, A.297, V.298 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.294 NAG.17: 9 residues within 4Å: Chain B: D.283, R.285, N.294, A.297, F.307, N.309, T.310, S.311, A.312 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:N.294, B:A.297, B:F.307 Hydrogen bonds: B:D.283, B:S.311 Water bridges: B:N.309, B:N.309 NAG.18: 5 residues within 4Å: Chain B: N.14, D.15, L.336, Y.337, N.338 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.15 Water bridges: B:D.15, B:N.338, B:N.338 NAG.19: 4 residues within 4Å: Chain A: I.371 Chain B: Y.350, N.352, V.353 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.353 Hydrogen bonds: B:N.352 NAG.20: 4 residues within 4Å: Chain B: F.70, N.72, I.128, T.130 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.70 Hydrogen bonds: B:N.72, B:I.128 Water bridges: B:T.130

2 x NA: SODIUM ION(Non-functional Binders)

NA.9: 6 residues within 4Å: Chain A: D.208, S.209, Q.210, S.256, E.258, L.260 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.209, A:S.256 Water bridges: A:L.260 NA.21: 6 residues within 4Å: Chain B: D.208, S.209, Q.210, S.256, E.258, L.260 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.209, B:L.260 Water bridges: B:L.260

2 x ZN: ZINC ION(Non-covalent)

ZN.10: 4 residues within 4Å: Chain A: E.31, H.35, D.39, H.319 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.31, A:E.31, A:H.35, A:D.39, A:H.319 ZN.22: 4 residues within 4Å: Chain B: E.31, H.35, D.39, H.319 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.31, B:E.31, B:H.35, B:D.39, B:H.319

4 x 6KL: methyl 4,5-bisacetamido-3,4,5-trideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid(Non-covalent)

6KL.11: 9 residues within 4Å: Chain A: D.22, A.23, Y.29, W.40, S.57, G.58, N.87, H.319, H.323 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.29, A:W.40 Hydrogen bonds: A:A.23, A:Y.29, A:S.57, A:G.58, A:N.87, A:H.323 6KL.12: 11 residues within 4Å: Chain A: L.97, I.144, Y.167, F.190, S.194, R.195, G.196, S.197, S.198, T.231, F.259 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.97, A:L.97, A:I.144, A:F.190, A:F.259, A:F.259 Hydrogen bonds: A:R.195, A:R.195, A:S.198, A:T.231 6KL.23: 9 residues within 4Å: Chain B: D.22, A.23, Y.29, W.40, S.57, G.58, N.87, H.319, H.323 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.29, B:W.40 Hydrogen bonds: B:A.23, B:S.57, B:G.58, B:N.87, B:H.323 6KL.24: 11 residues within 4Å: Chain B: L.97, I.144, Y.167, F.190, S.194, R.195, G.196, S.197, S.198, T.231, F.259 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.97, B:L.97, B:I.144, B:F.190, B:F.259, B:F.259 Hydrogen bonds: B:R.195, B:R.195, B:S.198

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bakkers, M.J. et al., Coronavirus receptor switch explained from the stereochemistry of protein-carbohydrate interactions and a single mutation. Proc.Natl.Acad.Sci.USA (2016)

Release Date

2016-05-11

Peptides

Hemagglutinin-esterase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Hemagglutinin-esterase

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