SMTL ID : 2yp2.1

Haemagglutinin of 2004 Human H3N2 Virus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

6 x NAG- NAG- MAN: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN.1: 4 residues within 4Å: Chain A: N.38, T.40, T.318, L.381 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.40 NAG-NAG-MAN.2: 7 residues within 4Å: Chain A: N.165, I.242 Chain C: S.219, P.221, R.222, D.225 Ligands: NAG-NAG.3 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:R.222 Water bridges: C:R.222 Hydrophobic interactions: A:I.242 NAG-NAG-MAN.12: 4 residues within 4Å: Chain B: N.38, T.40, T.318, L.381 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.40 NAG-NAG-MAN.13: 7 residues within 4Å: Chain A: S.219, P.221, R.222, D.225 Chain B: N.165, I.242 Ligands: NAG-NAG.14 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.222 Water bridges: A:R.222 Hydrophobic interactions: B:I.242 NAG-NAG-MAN.23: 4 residues within 4Å: Chain C: N.38, T.40, T.318, L.381 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.40 NAG-NAG-MAN.24: 7 residues within 4Å: Chain B: S.219, P.221, R.222, D.225 Chain C: N.165, I.242 Ligands: NAG-NAG.25 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:R.222 Water bridges: B:R.222 Hydrophobic interactions: C:I.242

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.3: 8 residues within 4Å: Chain A: A.163, L.164, N.165, R.201, N.246, S.247, T.248 Ligands: NAG-NAG-MAN.2 1 PLIP interactions: 1 interactions with chain C Water bridges: C:D.188 NAG-NAG.14: 8 residues within 4Å: Chain B: A.163, L.164, N.165, R.201, N.246, S.247, T.248 Ligands: NAG-NAG-MAN.13 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.188 NAG-NAG.25: 8 residues within 4Å: Chain C: A.163, L.164, N.165, R.201, N.246, S.247, T.248 Ligands: NAG-NAG-MAN.24 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.188

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

NAG.4: 3 residues within 4Å: Chain A: E.62, N.63, Y.94 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.63 Water bridges: A:N.63, A:K.92 NAG.5: 2 residues within 4Å: Chain A: N.133 Ligands: EPE.8 No protein-ligand interaction detected (PLIP) NAG.6: 4 residues within 4Å: Chain A: S.45, N.285, V.297, N.298 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.285, A:V.297, A:N.298 Water bridges: A:V.297 NAG.7: 5 residues within 4Å: Chain A: A.476, G.479, S.480, N.483, T.485 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.476, A:T.485 Water bridges: A:R.482 NAG.15: 3 residues within 4Å: Chain B: E.62, N.63, Y.94 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.63 Water bridges: B:N.63, B:K.92 NAG.16: 2 residues within 4Å: Chain B: N.133 Ligands: EPE.19 No protein-ligand interaction detected (PLIP) NAG.17: 4 residues within 4Å: Chain B: S.45, N.285, V.297, N.298 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.285, B:V.297, B:N.298 Water bridges: B:V.297 NAG.18: 5 residues within 4Å: Chain B: A.476, G.479, S.480, N.483, T.485 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.476, B:T.485 Water bridges: B:R.482 NAG.26: 3 residues within 4Å: Chain C: E.62, N.63, Y.94 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.63 Water bridges: C:N.63, C:K.92 NAG.27: 2 residues within 4Å: Chain C: N.133 Ligands: EPE.30 No protein-ligand interaction detected (PLIP) NAG.28: 4 residues within 4Å: Chain C: S.45, N.285, V.297, N.298 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.285, C:V.297, C:N.298 Water bridges: C:V.297 NAG.29: 5 residues within 4Å: Chain C: A.476, G.479, S.480, N.483, T.485 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:A.476, C:T.485 Water bridges: C:R.482

9 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.8: 11 residues within 4Å: Chain A: D.77, Q.80, R.141, R.142, S.146, F.147, F.148, S.149, L.151, R.255 Ligands: NAG.5 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.77, A:D.77, A:Q.80, A:L.151, A:R.255 Water bridges: A:S.149 Salt bridges: A:R.141, A:R.142 EPE.9: 6 residues within 4Å: Chain A: S.95, Y.98, P.99, Y.100, R.224, E.401 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.95, A:Y.98, A:Y.100, A:Y.100 Water bridges: A:R.224 Salt bridges: A:R.224 EPE.10: 5 residues within 4Å: Chain A: N.81, E.119, F.120, N.121, N.122 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.81, A:N.122, A:N.122 EPE.19: 11 residues within 4Å: Chain B: D.77, Q.80, R.141, R.142, S.146, F.147, F.148, S.149, L.151, R.255 Ligands: NAG.16 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.77, B:D.77, B:Q.80, B:L.151, B:R.255 Water bridges: B:S.149 Salt bridges: B:R.141, B:R.142 EPE.20: 6 residues within 4Å: Chain B: S.95, Y.98, P.99, Y.100, R.224, E.401 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.95, B:Y.98, B:Y.100, B:Y.100 Water bridges: B:R.224 Salt bridges: B:R.224 EPE.21: 5 residues within 4Å: Chain B: N.81, E.119, F.120, N.121, N.122 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.81, B:N.122, B:N.122 EPE.30: 11 residues within 4Å: Chain C: D.77, Q.80, R.141, R.142, S.146, F.147, F.148, S.149, L.151, R.255 Ligands: NAG.27 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:D.77, C:D.77, C:Q.80, C:L.151, C:R.255 Water bridges: C:S.149 Salt bridges: C:R.141, C:R.142 EPE.31: 6 residues within 4Å: Chain C: S.95, Y.98, P.99, Y.100, R.224, E.401 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.95, C:Y.98, C:Y.100, C:Y.100 Water bridges: C:R.224 Salt bridges: C:R.224 EPE.32: 5 residues within 4Å: Chain C: N.81, E.119, F.120, N.121, N.122 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.81, C:N.122, C:N.122

3 x TAM: TRIS(HYDROXYETHYL)AMINOMETHANE(Non-covalent)

TAM.11: 1 residues within 4Å: Chain C: E.426 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.383 TAM.22: 1 residues within 4Å: Chain A: E.426 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.383 TAM.33: 1 residues within 4Å: Chain B: E.426 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.383

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lin, Y.P. et al., Evolution of the Receptor Binding Properties of the Influenza A(H3N2) Hemagglutinin. Proc.Natl.Acad.Sci.USA (2012)

Release Date

2012-11-07

Peptides

HEMAGGLUTININ: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

HEMAGGLUTININ

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