SMTL ID : 2yp3.1

Haemagglutinin of 2004 Human H3N2 Virus in Complex with Human Receptor Analogue 6SLN

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 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: 8 residues within 4Å: Chain A: N.165, I.242 Chain B: T.187, S.219, P.221, R.222, D.225 Ligands: NAG-NAG.2 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.242 Hydrogen bonds: B:R.222 Water bridges: B:R.222 NAG-NAG-MAN.11: 8 residues within 4Å: Chain B: N.165, I.242 Chain C: T.187, S.219, P.221, R.222, D.225 Ligands: NAG-NAG.12 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:R.222 Water bridges: C:R.222 Hydrophobic interactions: B:I.242 NAG-NAG-MAN.21: 8 residues within 4Å: Chain A: T.187, S.219, P.221, R.222, D.225 Chain C: N.165, I.242 Ligands: NAG-NAG.22 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:I.242 Hydrogen bonds: A:R.222 Water bridges: A:R.222

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: 9 residues within 4Å: Chain A: A.163, L.164, N.165, R.201, N.246, S.247, T.248 Chain B: I.217 Ligands: NAG-NAG-MAN.1 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.188 NAG-NAG.12: 9 residues within 4Å: Chain B: A.163, L.164, N.165, R.201, N.246, S.247, T.248 Chain C: I.217 Ligands: NAG-NAG-MAN.11 1 PLIP interactions: 1 interactions with chain C Water bridges: C:D.188 NAG-NAG.22: 9 residues within 4Å: Chain A: I.217 Chain C: A.163, L.164, N.165, R.201, N.246, S.247, T.248 Ligands: NAG-NAG-MAN.21 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.188

3 x NAG- GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-GAL-SIA.3: 13 residues within 4Å: Chain A: Y.98, G.134, T.135, S.136, S.137, N.145, W.153, S.193, L.194, R.222, D.225, I.226, S.228 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.194, A:W.153, A:L.194 Hydrogen bonds: A:S.193, A:S.193, A:R.222, A:D.225, A:T.135, A:S.137, A:S.228, A:S.228 Water bridges: A:D.190, A:D.190, A:S.137, A:T.135, A:T.135, A:S.137, A:N.145 NAG-GAL-SIA.13: 13 residues within 4Å: Chain B: Y.98, G.134, T.135, S.136, S.137, N.145, W.153, S.193, L.194, R.222, D.225, I.226, S.228 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.194, B:W.153, B:L.194 Hydrogen bonds: B:S.193, B:S.193, B:R.222, B:D.225, B:T.135, B:S.137, B:S.228, B:S.228 Water bridges: B:D.190, B:D.190, B:S.137, B:T.135, B:T.135, B:S.137, B:N.145 NAG-GAL-SIA.23: 13 residues within 4Å: Chain C: Y.98, G.134, T.135, S.136, S.137, N.145, W.153, S.193, L.194, R.222, D.225, I.226, S.228 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:L.194, C:W.153, C:L.194 Hydrogen bonds: C:S.193, C:S.193, C:R.222, C:D.225, C:T.135, C:S.137, C:S.228, C:S.228 Water bridges: C:D.190, C:D.190, C:S.137, C:T.135, C:T.135, C:S.137, C:N.145

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

NAG.4: 3 residues within 4Å: Chain A: N.38, T.318, L.381 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.38, A:N.38, A:T.318 NAG.5: 3 residues within 4Å: Chain A: E.62, N.63, Y.94 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.63, A:Y.94 Water bridges: A:N.63, A:N.63, A:K.92 NAG.6: 2 residues within 4Å: Chain A: N.133 Ligands: EPE.8 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.132, A:N.133 NAG.7: 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.14: 3 residues within 4Å: Chain B: N.38, T.318, L.381 3 PLIP interactions: 3 interactions with chain B Water bridges: B:N.38, B:N.38, B:T.318 NAG.15: 3 residues within 4Å: Chain B: E.62, N.63, Y.94 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.63, B:Y.94 Water bridges: B:N.63, B:N.63, B:K.92 NAG.16: 2 residues within 4Å: Chain B: N.133 Ligands: EPE.18 2 PLIP interactions: 2 interactions with chain B Water bridges: B:Q.132, B:N.133 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.24: 3 residues within 4Å: Chain C: N.38, T.318, L.381 3 PLIP interactions: 3 interactions with chain C Water bridges: C:N.38, C:N.38, C:T.318 NAG.25: 3 residues within 4Å: Chain C: E.62, N.63, Y.94 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.63, C:Y.94 Water bridges: C:N.63, C:N.63, C:K.92 NAG.26: 2 residues within 4Å: Chain C: N.133 Ligands: EPE.28 2 PLIP interactions: 2 interactions with chain C Water bridges: C:Q.132, C:N.133 NAG.27: 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

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

EPE.8: 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.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.80, A:Q.80, A:R.255 Water bridges: A:N.152 Salt bridges: A:R.141 EPE.9: 5 residues within 4Å: Chain A: N.81, E.119, F.120, N.121, N.122 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.81, A:F.120, A:N.122, A:N.122 Water bridges: A:K.83, A:E.119 EPE.18: 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:R.255 Water bridges: B:N.152 Salt bridges: B:R.141 EPE.19: 5 residues within 4Å: Chain B: N.81, E.119, F.120, N.121, N.122 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.81, B:F.120, B:N.122, B:N.122 Water bridges: B:K.83, B:E.119 EPE.28: 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.26 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.80, C:Q.80, C:R.255 Water bridges: C:N.152 Salt bridges: C:R.141 EPE.29: 5 residues within 4Å: Chain C: N.81, E.119, F.120, N.121, N.122 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.81, C:F.120, C:N.122, C:N.122 Water bridges: C:K.83, C:E.119

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

TAM.10: 2 residues within 4Å: Chain A: R.383 Chain B: Y.423 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Y.423 Hydrogen bonds: A:R.383 Water bridges: A:R.383, A:E.432 TAM.20: 2 residues within 4Å: Chain B: R.383 Chain C: Y.423 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:R.383 Water bridges: B:R.383, B:E.432 Hydrophobic interactions: C:Y.423 TAM.30: 2 residues within 4Å: Chain A: Y.423 Chain C: R.383 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:Y.423 Hydrogen bonds: C:R.383 Water bridges: C:R.383, C:E.432

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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