SMTL ID : 4o5n.1

Crystal structure of A/Victoria/361/2011 (H3N2) influenza virus hemagglutinin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

hetero-3-3-mer

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: 3 residues within 4Å: Chain A: E.56, N.57, Y.88 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain C: E.56, N.57, Y.88 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 3 residues within 4Å: Chain E: E.56, N.57, Y.88 No protein-ligand interaction detected (PLIP)

3 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(Post Translational Modification)

NAG-NAG-BMA.2: 6 residues within 4Å: Chain A: N.159, I.236, L.238 Chain E: S.213, P.215, R.216 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: A:I.236 Hydrogen bonds: E:R.216 Water bridges: E:R.216 NAG-NAG-BMA.17: 6 residues within 4Å: Chain A: S.213, P.215, R.216 Chain C: N.159, I.236, L.238 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:I.236 Hydrogen bonds: A:R.216 Water bridges: A:R.216 NAG-NAG-BMA.32: 6 residues within 4Å: Chain C: S.213, P.215, R.216 Chain E: N.159, I.236, L.238 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:R.216 Water bridges: C:R.216 Hydrophobic interactions: E:I.236

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

NAG.3: 2 residues within 4Å: Chain A: N.16, N.32 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.16 NAG.4: 3 residues within 4Å: Chain A: N.32, T.312 Chain B: L.52 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.32, A:T.312 NAG.5: 4 residues within 4Å: Chain A: N.39, N.279, V.291, N.292 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.279, A:V.291, A:N.292 Water bridges: A:V.291 NAG.6: 2 residues within 4Å: Chain A: Q.126, N.127 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.127 NAG.18: 2 residues within 4Å: Chain C: N.16, N.32 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.16 NAG.19: 3 residues within 4Å: Chain C: N.32, T.312 Chain D: L.52 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.32, C:T.312 NAG.20: 4 residues within 4Å: Chain C: N.39, N.279, V.291, N.292 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.279, C:V.291, C:N.292 Water bridges: C:V.291 NAG.21: 2 residues within 4Å: Chain C: Q.126, N.127 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.127 NAG.33: 2 residues within 4Å: Chain E: N.16, N.32 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.16 NAG.34: 3 residues within 4Å: Chain E: N.32, T.312 Chain F: L.52 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.32, E:T.312 NAG.35: 4 residues within 4Å: Chain E: N.39, N.279, V.291, N.292 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:N.279, E:V.291, E:N.292 Water bridges: E:V.291 NAG.36: 2 residues within 4Å: Chain E: Q.126, N.127 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.127

24 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain A: P.287, R.301 Chain B: W.92 Chain F: Y.94 Ligands: GOL.10 Ligand excluded by PLIP GOL.8: 3 residues within 4Å: Chain A: Y.99 Chain B: E.72 Chain C: R.202 Ligand excluded by PLIP GOL.10: 7 residues within 4Å: Chain B: R.54, L.55, L.99 Chain F: Y.94, E.97, L.98 Ligands: GOL.7 Ligand excluded by PLIP GOL.11: 3 residues within 4Å: Chain B: V.161, Y.162, E.165 Ligand excluded by PLIP GOL.12: 4 residues within 4Å: Chain B: R.25, R.32, G.33, Q.34 Ligand excluded by PLIP GOL.13: 5 residues within 4Å: Chain B: F.9, E.11, M.133, G.134, N.135 Ligand excluded by PLIP GOL.14: 5 residues within 4Å: Chain B: Q.42, A.43, D.46, Q.47 Ligands: GOL.15 Ligand excluded by PLIP GOL.15: 5 residues within 4Å: Chain B: K.39, A.43, E.114, K.117 Ligands: GOL.14 Ligand excluded by PLIP GOL.22: 5 residues within 4Å: Chain B: Y.94 Chain C: P.287, R.301 Chain D: W.92 Ligands: GOL.25 Ligand excluded by PLIP GOL.23: 3 residues within 4Å: Chain C: Y.99 Chain D: E.72 Chain E: R.202 Ligand excluded by PLIP GOL.25: 7 residues within 4Å: Chain B: Y.94, E.97, L.98 Chain D: R.54, L.55, L.99 Ligands: GOL.22 Ligand excluded by PLIP GOL.26: 3 residues within 4Å: Chain D: V.161, Y.162, E.165 Ligand excluded by PLIP GOL.27: 4 residues within 4Å: Chain D: R.25, R.32, G.33, Q.34 Ligand excluded by PLIP GOL.28: 5 residues within 4Å: Chain D: F.9, E.11, M.133, G.134, N.135 Ligand excluded by PLIP GOL.29: 5 residues within 4Å: Chain D: Q.42, A.43, D.46, Q.47 Ligands: GOL.30 Ligand excluded by PLIP GOL.30: 5 residues within 4Å: Chain D: K.39, A.43, E.114, K.117 Ligands: GOL.29 Ligand excluded by PLIP GOL.37: 5 residues within 4Å: Chain D: Y.94 Chain E: P.287, R.301 Chain F: W.92 Ligands: GOL.40 Ligand excluded by PLIP GOL.38: 3 residues within 4Å: Chain A: R.202 Chain E: Y.99 Chain F: E.72 Ligand excluded by PLIP GOL.40: 7 residues within 4Å: Chain D: Y.94, E.97, L.98 Chain F: R.54, L.55, L.99 Ligands: GOL.37 Ligand excluded by PLIP GOL.41: 3 residues within 4Å: Chain F: V.161, Y.162, E.165 Ligand excluded by PLIP GOL.42: 4 residues within 4Å: Chain F: R.25, R.32, G.33, Q.34 Ligand excluded by PLIP GOL.43: 5 residues within 4Å: Chain F: F.9, E.11, M.133, G.134, N.135 Ligand excluded by PLIP GOL.44: 5 residues within 4Å: Chain F: Q.42, A.43, D.46, Q.47 Ligands: GOL.45 Ligand excluded by PLIP GOL.45: 5 residues within 4Å: Chain F: K.39, A.43, E.114, K.117 Ligands: GOL.44 Ligand excluded by PLIP

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.9: 7 residues within 4Å: Chain A: H.12 Chain B: M.17, V.18, D.19, G.20, W.21, I.45 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:M.17 Water bridges: B:D.19, B:Q.42 PEG.24: 7 residues within 4Å: Chain C: H.12 Chain D: M.17, V.18, D.19, G.20, W.21, I.45 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:M.17 Water bridges: D:D.19, D:Q.42 PEG.39: 7 residues within 4Å: Chain E: H.12 Chain F: M.17, V.18, D.19, G.20, W.21, I.45 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:M.17 Water bridges: F:D.19, F:Q.42

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, P.S. et al., Receptor mimicry by antibody F045-092 facilitates universal binding to the H3 subtype of influenza virus. Nat Commun (2014)

Release Date

2014-04-16

Peptides

Hemagglutinin HA1 chain: ACE
Hemagglutinin HA2 chain: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
B

D
B

F
B

Hemagglutinin HA1 chain

Hemagglutinin HA2 chain

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