SMTL ID : 4wea.1

Structure and receptor binding prefereneces of recombinant human A(H3N2) virus hemagglutinins

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-trimer

Ligands

3 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: 6 residues within 4Å: Chain A: N.170, T.172 Chain B: S.224, P.226, R.227 Ligands: NAG.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.227 NAG-NAG.10: 6 residues within 4Å: Chain B: N.170, T.172 Chain C: S.224, P.226, R.227 Ligands: NAG.15 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.227 NAG-NAG.19: 6 residues within 4Å: Chain A: S.224, P.226, R.227 Chain C: N.170, T.172 Ligands: NAG.24 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.227

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

NAG.2: 4 residues within 4Å: Chain A: N.27, T.29, N.43 Ligands: NAG.3 Ligand excluded by PLIP NAG.3: 4 residues within 4Å: Chain A: N.43, T.323, L.386 Ligands: NAG.2 Ligand excluded by PLIP NAG.4: 3 residues within 4Å: Chain A: E.67, N.68, Y.99 Ligand excluded by PLIP NAG.5: 2 residues within 4Å: Chain A: Q.137, N.138 Ligand excluded by PLIP NAG.6: 6 residues within 4Å: Chain A: A.168, L.169, N.251, T.253 Chain B: G.223 Ligands: NAG-NAG.1 Ligand excluded by PLIP NAG.7: 5 residues within 4Å: Chain A: N.50, N.290, V.302, N.303, E.403 Ligand excluded by PLIP NAG.8: 5 residues within 4Å: Chain A: A.481, G.484, S.485, N.488, T.490 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain B: N.27, T.29, N.43 Ligands: NAG.12 Ligand excluded by PLIP NAG.12: 4 residues within 4Å: Chain B: N.43, T.323, L.386 Ligands: NAG.11 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain B: E.67, N.68, Y.99 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain B: Q.137, N.138 Ligand excluded by PLIP NAG.15: 6 residues within 4Å: Chain B: A.168, L.169, N.251, T.253 Chain C: G.223 Ligands: NAG-NAG.10 Ligand excluded by PLIP NAG.16: 5 residues within 4Å: Chain B: N.50, N.290, V.302, N.303, E.403 Ligand excluded by PLIP NAG.17: 5 residues within 4Å: Chain B: A.481, G.484, S.485, N.488, T.490 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain C: N.27, T.29, N.43 Ligands: NAG.21 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain C: N.43, T.323, L.386 Ligands: NAG.20 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain C: E.67, N.68, Y.99 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain C: Q.137, N.138 Ligand excluded by PLIP NAG.24: 6 residues within 4Å: Chain A: G.223 Chain C: A.168, L.169, N.251, T.253 Ligands: NAG-NAG.19 Ligand excluded by PLIP NAG.25: 5 residues within 4Å: Chain C: N.50, N.290, V.302, N.303, E.403 Ligand excluded by PLIP NAG.26: 5 residues within 4Å: Chain C: A.481, G.484, S.485, N.488, T.490 Ligand excluded by PLIP

3 x SIA: N-acetyl-alpha-neuraminic acid(Non-covalent)

SIA.9: 9 residues within 4Å: Chain A: G.139, T.140, S.141, S.142, W.158, T.160, D.195, F.198, L.199 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.158, A:T.160, A:L.199 Hydrogen bonds: A:S.142, A:D.195 SIA.18: 9 residues within 4Å: Chain B: G.139, T.140, S.141, S.142, W.158, T.160, D.195, F.198, L.199 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.158, B:T.160, B:L.199 Hydrogen bonds: B:S.142, B:D.195 SIA.27: 9 residues within 4Å: Chain C: G.139, T.140, S.141, S.142, W.158, T.160, D.195, F.198, L.199 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:W.158, C:T.160, C:L.199 Hydrogen bonds: C:S.142, C:D.195

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, H. et al., Structure and receptor binding preferences of recombinant human A(H3N2) virus hemagglutinins. Virology (2015)

Release Date

2015-02-11

Peptides

Hemagglutinin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Hemagglutinin

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