SMTL ID : 4zxn.1

Crystal structure of rat coronavirus strain New-Jersey Hemagglutinin-Esterase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: A.134, Y.135, G.136, N.174, K.253 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.174, A:K.253 NAG.2: 5 residues within 4Å: Chain A: S.209, N.224, L.257, E.258 Chain B: Y.213 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.209, A:E.258 Hydrophobic interactions: B:Y.213 NAG.3: 8 residues within 4Å: Chain A: N.287, S.288, T.289, D.313, Y.314, S.315, G.316, V.321 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.289 Hydrogen bonds: A:D.313, A:G.316, A:G.316 Water bridges: A:S.315 NAG.4: 3 residues within 4Å: Chain A: N.294, A.297, V.298 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.297 Hydrogen bonds: A:N.294 NAG.5: 4 residues within 4Å: Chain A: D.15, L.336, Y.337, N.338 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.15 NAG.6: 5 residues within 4Å: Chain A: Y.350, N.352, V.353 Chain B: N.370, I.371 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.353 Hydrogen bonds: A:N.352 NAG.9: 5 residues within 4Å: Chain B: A.134, Y.135, G.136, N.174, K.253 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.174, B:K.253 NAG.10: 5 residues within 4Å: Chain A: Y.213 Chain B: S.209, N.224, L.257, E.258 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.213 Hydrogen bonds: B:S.209, B:E.258, B:E.258 NAG.11: 8 residues within 4Å: Chain B: N.287, S.288, T.289, D.313, Y.314, S.315, G.316, V.321 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:T.289 Hydrogen bonds: B:D.313, B:G.316, B:G.316 Water bridges: B:S.315 NAG.12: 3 residues within 4Å: Chain B: N.294, A.297, V.298 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.297 Hydrogen bonds: B:N.294 NAG.13: 4 residues within 4Å: Chain B: D.15, L.336, Y.337, N.338 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.15 NAG.14: 5 residues within 4Å: Chain A: N.370, 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

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

NA.7: 7 residues within 4Å: Chain A: D.208, S.209, Q.210, S.256, E.258, F.259, L.260 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.209, A:S.256 NA.15: 7 residues within 4Å: Chain B: D.208, S.209, Q.210, S.256, E.258, F.259, L.260 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.209, B:L.260

2 x ZN: ZINC ION(Non-covalent)

ZN.8: 5 residues within 4Å: Chain A: E.31, H.35, D.39, W.40, H.319 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.31, A:H.35, A:D.39, A:D.39, A:H.319 ZN.16: 5 residues within 4Å: Chain B: E.31, H.35, D.39, W.40, H.319 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.31, B:H.35, B:D.39, B:D.39, B:H.319

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bakkers, M.J.G. et al., Crystal structures of murine coronavirus hemagglutinin-esterases reveal structural basis for esterase substrate specificity. To Be Published

Release Date

2016-05-11

Peptides

HE protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

HE protein

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