SMTL ID : 2yp7.1

Haemagglutinin of 2005 Human H3N2 Virus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-trimer

Ligands

3 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: 7 residues within 4Å: Chain A: N.165, I.242 Chain B: S.219, P.221, R.222, N.225 Ligands: NAG-NAG.2 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.222 Water bridges: B:R.222 Hydrophobic interactions: A:I.242 NAG-NAG-MAN.12: 7 residues within 4Å: Chain B: N.165, I.242 Chain C: S.219, P.221, R.222, N.225 Ligands: NAG-NAG.13 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:I.242 Hydrogen bonds: C:R.222 Water bridges: C:R.222 NAG-NAG-MAN.23: 7 residues within 4Å: Chain A: S.219, P.221, R.222, N.225 Chain C: N.165, I.242 Ligands: NAG-NAG.24 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:R.222 Water bridges: A: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.2: 8 residues within 4Å: Chain A: A.163, L.164, N.165, R.201, N.246, S.247, T.248 Ligands: NAG-NAG-MAN.1 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.188 NAG-NAG.13: 8 residues within 4Å: Chain B: A.163, L.164, N.165, R.201, N.246, S.247, T.248 Ligands: NAG-NAG-MAN.12 1 PLIP interactions: 1 interactions with chain C Water bridges: C:D.188 NAG-NAG.24: 8 residues within 4Å: Chain C: A.163, L.164, N.165, R.201, N.246, S.247, T.248 Ligands: NAG-NAG-MAN.23 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.188

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

NAG.3: 3 residues within 4Å: Chain A: N.38, T.318, L.381 Ligand excluded by PLIP NAG.4: 3 residues within 4Å: Chain A: E.62, N.63, Y.94 Ligand excluded by PLIP NAG.5: 2 residues within 4Å: Chain A: N.133 Ligands: EPE.9 Ligand excluded by PLIP NAG.6: 5 residues within 4Å: Chain A: S.45, N.285, V.297, N.298, E.398 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: N.126, T.128 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain A: G.479, R.482, N.483 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain B: N.38, T.318, L.381 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain B: E.62, N.63, Y.94 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain B: N.133 Ligands: EPE.20 Ligand excluded by PLIP NAG.17: 5 residues within 4Å: Chain B: S.45, N.285, V.297, N.298, E.398 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: N.126, T.128 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain B: G.479, R.482, N.483 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain C: N.38, T.318, L.381 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain C: E.62, N.63, Y.94 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain C: N.133 Ligands: EPE.31 Ligand excluded by PLIP NAG.28: 5 residues within 4Å: Chain C: S.45, N.285, V.297, N.298, E.398 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain C: N.126, T.128 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: G.479, R.482, N.483 Ligand excluded by PLIP

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

EPE.9: 10 residues within 4Å: Chain A: D.77, Q.80, R.141, S.146, F.147, F.148, S.149, L.151, R.255 Ligands: NAG.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.80, A:Q.80, A:L.151, A:R.255 Salt bridges: A:R.141 EPE.10: 9 residues within 4Å: Chain A: S.95, Y.98, P.99, Y.100, Y.105, V.223, R.224, E.401 Chain C: R.208 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:S.95, A:Y.100, A:Y.100, A:E.401, C:R.208 Water bridges: A:S.95, A:R.224 Salt bridges: A:R.224 pi-Cation interactions: A:Y.105 EPE.20: 10 residues within 4Å: Chain B: D.77, Q.80, R.141, S.146, F.147, F.148, S.149, L.151, R.255 Ligands: NAG.16 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.80, B:Q.80, B:L.151, B:R.255 Salt bridges: B:R.141 EPE.21: 9 residues within 4Å: Chain A: R.208 Chain B: S.95, Y.98, P.99, Y.100, Y.105, V.223, R.224, E.401 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.95, B:Y.100, B:Y.100, B:E.401, A:R.208 Water bridges: B:S.95, B:R.224 Salt bridges: B:R.224 pi-Cation interactions: B:Y.105 EPE.31: 10 residues within 4Å: Chain C: D.77, Q.80, R.141, S.146, F.147, F.148, S.149, L.151, R.255 Ligands: NAG.27 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.80, C:Q.80, C:L.151, C:R.255 Salt bridges: C:R.141 EPE.32: 9 residues within 4Å: Chain B: R.208 Chain C: S.95, Y.98, P.99, Y.100, Y.105, V.223, R.224, E.401 9 PLIP interactions: 1 interactions with chain B, 8 interactions with chain C Hydrogen bonds: B:R.208, C:S.95, C:Y.100, C:Y.100, C:E.401 Water bridges: C:S.95, C:R.224 Salt bridges: C:R.224 pi-Cation interactions: C:Y.105

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

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