SMTL ID : 7jpd.1 (1 other biounit)

Crystal structure of the trimeric full length mature hemagglutinin from influenza A virus A/Fort Monmouth/1/1947

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.95 Å

Oligo State

hetero-3-3-mer

Ligands

1 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

NAG-NAG-BMA.1: 7 residues within 4Å: Chain A: N.66, E.68, N.89, C.92, S.139, R.223 Ligands: IOD.11 No protein-ligand interaction detected (PLIP)

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: 3 residues within 4Å: Chain A: N.129, T.131, R.132 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain C: N.129, T.131, R.132, T.156 Ligands: IOD.34 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain E: N.129, T.131, R.132, T.156 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA-MAN-MAN.3: 9 residues within 4Å: Chain C: N.66, E.68, E.88, N.89, C.92, K.221, R.223, G.224 Ligands: IOD.24 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.223, C:K.221, C:G.224 NAG-NAG-BMA-MAN-MAN.5: 7 residues within 4Å: Chain E: N.66, E.68, N.89, C.92, R.223 Ligands: IOD.39, IOD.48 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.223

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

NAG.7: 1 residues within 4Å: Chain A: N.25 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.25 NAG.22: 1 residues within 4Å: Chain C: N.25 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.25, C:T.27 NAG.36: 1 residues within 4Å: Chain E: N.25 No protein-ligand interaction detected (PLIP) NAG.37: 1 residues within 4Å: Chain E: N.157 No protein-ligand interaction detected (PLIP)

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 3 residues within 4Å: Chain A: D.16, H.30, S.31 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.16, A:S.31

40 x IOD: IODIDE ION(Non-functional Binders)

IOD.9: 3 residues within 4Å: Chain A: D.19, R.315 Chain B: V.100 Ligand excluded by PLIP IOD.10: 4 residues within 4Å: Chain A: G.55, C.57, C.69, E.70 Ligand excluded by PLIP IOD.11: 4 residues within 4Å: Chain A: E.88, G.90, T.91 Ligands: NAG-NAG-BMA.1 Ligand excluded by PLIP IOD.12: 2 residues within 4Å: Chain A: K.196, N.247 Ligand excluded by PLIP IOD.13: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.14: 2 residues within 4Å: Chain A: Y.93, H.182 Ligand excluded by PLIP IOD.15: 2 residues within 4Å: Chain A: K.191, R.195 Ligand excluded by PLIP IOD.16: 2 residues within 4Å: Chain A: D.278, T.279 Ligand excluded by PLIP IOD.17: 2 residues within 4Å: Chain A: R.321 Chain B: G.1 Ligand excluded by PLIP IOD.18: 3 residues within 4Å: Chain A: D.16, T.17, R.315 Ligand excluded by PLIP IOD.19: 3 residues within 4Å: Chain A: K.280, E.304 Chain B: F.63 Ligand excluded by PLIP IOD.20: 4 residues within 4Å: Chain A: W.62, L.72, R.115, F.257 Ligand excluded by PLIP IOD.21: 2 residues within 4Å: Chain A: P.94, G.95 Ligand excluded by PLIP IOD.23: 4 residues within 4Å: Chain C: G.55, C.57, C.69, E.70 Ligand excluded by PLIP IOD.24: 5 residues within 4Å: Chain C: E.88, G.90, T.91, C.92 Ligands: NAG-NAG-BMA-MAN-MAN.3 Ligand excluded by PLIP IOD.25: 1 residues within 4Å: Chain C: N.247 Ligand excluded by PLIP IOD.26: 1 residues within 4Å: Chain C: L.163 Ligand excluded by PLIP IOD.27: 1 residues within 4Å: Chain C: H.182 Ligand excluded by PLIP IOD.28: 1 residues within 4Å: Chain C: R.195 Ligand excluded by PLIP IOD.29: 2 residues within 4Å: Chain C: R.321 Chain D: L.108 Ligand excluded by PLIP IOD.30: 2 residues within 4Å: Chain C: L.72, R.115 Ligand excluded by PLIP IOD.31: 2 residues within 4Å: Chain C: P.94, G.95 Ligand excluded by PLIP IOD.32: 2 residues within 4Å: Chain C: T.17, R.315 Ligand excluded by PLIP IOD.33: 3 residues within 4Å: Chain C: D.19, R.315 Chain D: V.100 Ligand excluded by PLIP IOD.34: 3 residues within 4Å: Chain C: N.129, I.130 Ligands: NAG-NAG.4 Ligand excluded by PLIP IOD.35: 3 residues within 4Å: Chain D: Q.30, N.145, E.147 Ligand excluded by PLIP IOD.38: 2 residues within 4Å: Chain E: G.55, C.57 Ligand excluded by PLIP IOD.39: 4 residues within 4Å: Chain E: E.88, G.90, T.91 Ligands: NAG-NAG-BMA-MAN-MAN.5 Ligand excluded by PLIP IOD.40: 1 residues within 4Å: Chain E: K.127 Ligand excluded by PLIP IOD.41: 2 residues within 4Å: Chain E: Y.93, H.182 Ligand excluded by PLIP IOD.42: 2 residues within 4Å: Chain E: K.191, R.195 Ligand excluded by PLIP IOD.43: 1 residues within 4Å: Chain E: N.247 Ligand excluded by PLIP IOD.44: 1 residues within 4Å: Chain E: D.278 Ligand excluded by PLIP IOD.45: 2 residues within 4Å: Chain E: P.94, G.95 Ligand excluded by PLIP IOD.46: 4 residues within 4Å: Chain E: D.19, K.313, R.315 Chain F: V.100 Ligand excluded by PLIP IOD.47: 3 residues within 4Å: Chain E: D.16, T.17, R.315 Ligand excluded by PLIP IOD.48: 3 residues within 4Å: Chain E: G.224 Ligands: NAG-NAG-BMA-MAN-MAN.5, NAG-NAG-BMA-MAN-MAN.5 Ligand excluded by PLIP IOD.49: 2 residues within 4Å: Chain E: I.268, T.269 Ligand excluded by PLIP IOD.50: 2 residues within 4Å: Chain E: R.321 Chain F: L.108 Ligand excluded by PLIP IOD.51: 1 residues within 4Å: Chain F: E.147 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ghafoori, S.M. et al., Structural characterisation of hemagglutinin from seven Influenza A H1N1 strains reveal diversity in the C05 antibody recognition site. Sci Rep (2023)

Release Date

2021-10-06

Peptides

Hemagglutinin HA1 chain: ACE
Hemagglutinin HA2 chain: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
D

E
E

B
a

D
d

F
e

Hemagglutinin HA1 chain

Hemagglutinin HA2 chain

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