SMTL ID : 7jpd.2 (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

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: 7 residues within 4Å: Chain A: N.66, E.68, E.88, N.89, C.92, R.223 Ligands: IOD.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.223 NAG-NAG.3: 5 residues within 4Å: Chain C: N.129, T.131, R.132, T.156 Ligands: IOD.30 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain E: N.129, 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.2: 9 residues within 4Å: Chain C: N.66, E.68, E.88, N.89, C.92, S.139, K.221, R.223 Ligands: IOD.22 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.223, C:R.223 NAG-NAG-BMA-MAN-MAN.4: 11 residues within 4Å: Chain E: N.66, E.68, E.88, N.89, C.92, S.139, K.221, R.223, G.224 Ligands: IOD.38, IOD.48 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.223, E:K.221, E:G.224

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

NAG.6: 1 residues within 4Å: Chain A: N.25 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.25 NAG.7: 4 residues within 4Å: Chain A: N.129, T.131, R.132, T.156 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.129, A:T.131, A:R.132 NAG.8: 1 residues within 4Å: Chain A: N.13 No protein-ligand interaction detected (PLIP) NAG.19: 1 residues within 4Å: Chain C: N.25 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.25 NAG.20: 1 residues within 4Å: Chain C: N.157 No protein-ligand interaction detected (PLIP) NAG.34: 1 residues within 4Å: Chain E: N.25 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.25 NAG.35: 1 residues within 4Å: Chain E: N.157 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.157

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

IOD.9: 2 residues within 4Å: Chain A: G.55, C.57 Ligand excluded by PLIP IOD.10: 3 residues within 4Å: Chain A: E.88, G.90 Ligands: NAG-NAG.1 Ligand excluded by PLIP IOD.11: 2 residues within 4Å: Chain A: Y.93, H.182 Ligand excluded by PLIP IOD.12: 2 residues within 4Å: Chain A: K.191, R.195 Ligand excluded by PLIP IOD.13: 3 residues within 4Å: Chain A: D.278, T.279, K.280 Ligand excluded by PLIP IOD.14: 3 residues within 4Å: Chain A: R.321 Chain B: G.1, L.108 Ligand excluded by PLIP IOD.15: 2 residues within 4Å: Chain A: D.16, T.17 Ligand excluded by PLIP IOD.16: 4 residues within 4Å: Chain A: D.19, K.313, R.315 Chain B: V.100 Ligand excluded by PLIP IOD.17: 2 residues within 4Å: Chain A: P.94, G.95 Ligand excluded by PLIP IOD.18: 3 residues within 4Å: Chain B: Q.30, N.145, E.147 Ligand excluded by PLIP IOD.21: 3 residues within 4Å: Chain C: G.55, C.69, E.70 Ligand excluded by PLIP IOD.22: 3 residues within 4Å: Chain C: E.88, G.90 Ligands: NAG-NAG-BMA-MAN-MAN.2 Ligand excluded by PLIP IOD.23: 1 residues within 4Å: Chain C: N.247 Ligand excluded by PLIP IOD.24: 1 residues within 4Å: Chain C: L.163 Ligand excluded by PLIP IOD.25: 2 residues within 4Å: Chain C: Y.93, H.182 Ligand excluded by PLIP IOD.26: 2 residues within 4Å: Chain C: K.191, R.195 Ligand excluded by PLIP IOD.27: 4 residues within 4Å: Chain C: D.19, K.313, R.315 Chain D: V.100 Ligand excluded by PLIP IOD.28: 3 residues within 4Å: Chain C: T.17, K.313, R.315 Ligand excluded by PLIP IOD.29: 2 residues within 4Å: Chain C: P.94, G.95 Ligand excluded by PLIP IOD.30: 3 residues within 4Å: Chain C: N.129, I.130 Ligands: NAG-NAG.3 Ligand excluded by PLIP IOD.31: 4 residues within 4Å: Chain C: R.321 Chain D: G.1, I.6, L.108 Ligand excluded by PLIP IOD.32: 3 residues within 4Å: Chain D: Q.30, N.145, E.147 Ligand excluded by PLIP IOD.33: 1 residues within 4Å: Chain E: L.22 Ligand excluded by PLIP IOD.36: 4 residues within 4Å: Chain E: L.54, G.55, C.57, E.70 Ligand excluded by PLIP IOD.37: 1 residues within 4Å: Chain E: L.72 Ligand excluded by PLIP IOD.38: 5 residues within 4Å: Chain E: E.88, G.90, T.91, C.92 Ligands: NAG-NAG-BMA-MAN-MAN.4 Ligand excluded by PLIP IOD.39: 1 residues within 4Å: Chain E: N.247 Ligand excluded by PLIP IOD.40: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.41: 2 residues within 4Å: Chain E: Y.93, H.182 Ligand excluded by PLIP IOD.42: 1 residues within 4Å: Chain E: R.195 Ligand excluded by PLIP IOD.43: 1 residues within 4Å: Chain E: D.278 Ligand excluded by PLIP IOD.44: 2 residues within 4Å: Chain E: R.321 Chain F: L.108 Ligand excluded by PLIP IOD.45: 2 residues within 4Å: Chain E: D.19, R.315 Ligand excluded by PLIP IOD.46: 3 residues within 4Å: Chain E: T.17, K.313, R.315 Ligand excluded by PLIP IOD.47: 2 residues within 4Å: Chain E: P.94, G.95 Ligand excluded by PLIP IOD.48: 2 residues within 4Å: Ligands: NAG-NAG-BMA-MAN-MAN.4, NAG-NAG-BMA-MAN-MAN.4 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
B

C
C

E
F

B
b

D
c

F
f

Hemagglutinin HA1 chain

Hemagglutinin HA2 chain

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