SMTL ID : 2ypg.1

Haemagglutinin of 1968 Human H3N2 Virus in Complex with Human Receptor Analogue LSTc

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

hetero-3-3-mer

Ligands

1 x NAG- NAG- FUL: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG-FUL.1: 5 residues within 4Å: Chain A: Q.80, N.81, E.119, F.120, I.121 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG-BMA.2: 7 residues within 4Å: Chain A: N.165, T.167, V.242 Chain E: S.219, R.220, P.221, W.222 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:W.222 Hydrophobic interactions: A:V.242 NAG-NAG-BMA.7: 8 residues within 4Å: Chain A: T.187, S.219, R.220, P.221, W.222 Chain C: N.165, T.167 Ligands: FLC.22 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.222

5 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: 5 residues within 4Å: Chain A: S.45, N.285, V.297, N.298 Chain B: E.69 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain B: A.147, E.150, N.154, T.156 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain C: Q.80, N.81, E.119, F.120 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain C: S.45, N.285, V.297, N.298 Chain D: E.69 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain E: S.45, N.285, V.297, N.298 Chain F: E.69 No protein-ligand interaction detected (PLIP)

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

BGC-GAL-NAG-GAL-SIA.4: 13 residues within 4Å: Chain A: Y.98, G.134, G.135, S.136, N.137, W.153, K.156, H.183, E.190, S.193, L.194, L.226, S.228 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.156, A:S.193, A:Y.98, A:G.135, A:N.137, A:N.137, A:H.183, A:S.228 Salt bridges: A:K.156 BGC-GAL-NAG-GAL-SIA.12: 13 residues within 4Å: Chain E: Y.98, G.134, G.135, S.136, N.137, W.153, K.156, H.183, E.190, L.194, G.225, L.226, S.228 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:G.225, E:G.135, E:N.137, E:N.137, E:E.190, E:S.228 Hydrophobic interactions: E:W.153

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

GAL-NAG-GAL-SIA.9: 13 residues within 4Å: Chain C: Y.98, G.134, G.135, S.136, N.137, W.153, H.183, E.190, L.194, W.222, G.225, L.226, S.228 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:G.225, C:G.135, C:N.137, C:N.137, C:H.183, C:S.228 Water bridges: C:S.228

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG-BMA.10: 5 residues within 4Å: Chain C: S.219, P.221, W.222 Chain E: N.165, T.167 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain C Hydrophobic interactions: E:T.167 Hydrogen bonds: C:W.222

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

NAG.13: 3 residues within 4Å: Chain A: N.38, T.318 Chain B: L.52 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.318 NAG.19: 3 residues within 4Å: Chain C: N.38, T.318 Chain D: L.52 1 PLIP interactions: 1 interactions with chain C Water bridges: C:N.38 NAG.23: 4 residues within 4Å: Chain D: A.147, E.150, N.154, T.156 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.154 NAG.25: 5 residues within 4Å: Chain E: Q.80, N.81, E.119, F.120, I.121 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.119 NAG.29: 4 residues within 4Å: Chain F: A.147, E.150, N.154, T.156 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.154

13 x FLC: CITRATE ANION(Non-covalent)

FLC.14: 4 residues within 4Å: Chain A: I.34, R.321 Chain B: A.7 Chain D: Q.47 4 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: D:Q.47 Salt bridges: D:K.117, A:R.321 Water bridges: B:G.1 FLC.15: 4 residues within 4Å: Chain A: T.128, V.163, L.164, N.165 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.128, A:T.128, A:V.163, A:N.165 FLC.16: 6 residues within 4Å: Chain B: Y.94, E.97, L.98 Chain D: R.54, V.55, L.99 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.54 Salt bridges: D:R.54, D:R.54 FLC.17: 6 residues within 4Å: Chain B: R.54, V.55, K.58, L.99 Chain F: Y.94, E.97 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:K.307 Hydrogen bonds: B:R.54 Salt bridges: B:R.54 FLC.18: 4 residues within 4Å: Chain A: R.269 Chain B: E.69, F.70, S.71 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Salt bridges: A:R.269, A:R.269 Hydrogen bonds: B:E.69, B:S.71 FLC.20: 5 residues within 4Å: Chain C: D.31, R.321 Chain D: A.7 Chain F: A.43, Q.47 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain F Salt bridges: C:R.321 Hydrogen bonds: F:Q.47 FLC.21: 5 residues within 4Å: Chain A: Y.100, D.101, V.102, Y.105 Chain C: R.208 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:Y.105 Hydrogen bonds: A:S.95, A:V.102, C:R.208 Water bridges: A:Y.100 Salt bridges: C:R.208, C:R.208 FLC.22: 6 residues within 4Å: Chain C: T.126, T.128, N.165, V.166, T.167 Ligands: NAG-NAG-BMA.7 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.167 FLC.24: 7 residues within 4Å: Chain D: Y.94, E.97, L.98 Chain E: P.293 Chain F: R.54, V.55, L.99 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain D Hydrophobic interactions: F:L.99, F:L.99, D:Y.94 Salt bridges: F:R.54 FLC.26: 5 residues within 4Å: Chain B: Q.47 Chain E: D.31, I.34, R.321 Chain F: A.7 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain E, 2 interactions with chain F Salt bridges: B:K.117, E:R.321 Hydrogen bonds: E:D.31 Water bridges: F:G.1, F:G.1 FLC.27: 4 residues within 4Å: Chain E: D.77, Q.80, R.141, S.149 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:Q.80 Water bridges: E:R.255 Salt bridges: E:R.141, E:R.150, E:R.255 FLC.28: 3 residues within 4Å: Chain E: T.40, E.41, K.292 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:T.40, E:E.41, E:K.292 Salt bridges: E:K.292, E:K.292, E:K.292 FLC.30: 3 residues within 4Å: Chain B: R.123 Chain D: R.123 Chain F: R.123 8 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B, 4 interactions with chain F Water bridges: D:R.123, F:R.123, F:R.123 Salt bridges: D:R.123, B:R.123, F:R.123, F:R.123 Hydrogen bonds: B:R.123

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 HA1 CHAIN: ACE
HEMAGGLUTININ HA2 CHAIN: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

HEMAGGLUTININ HA1 CHAIN

HEMAGGLUTININ HA2 CHAIN

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