SMTL ID : 6lks.2 (1 other biounit)

Effects of zinc ion on oligomerization and pH stability of influenza virus hemagglutinin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.24 Å

Oligo State

hetero-3-3-mer

Ligands

4 x NAG- NAG- BMA- MAN: 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.1: 3 residues within 4Å: Chain A: G.57, N.58 Ligands: NAG-NAG-BMA-MAN-NAG.2 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.3: 3 residues within 4Å: Chain C: G.57, N.58 Ligands: NAG-NAG-BMA-MAN.4 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.4: 9 residues within 4Å: Chain C: N.68, E.90, N.91, C.94, S.138, C.139, R.224, D.225 Ligands: NAG-NAG-BMA-MAN.3 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.224 NAG-NAG-BMA-MAN.6: 9 residues within 4Å: Chain E: N.58, N.68, E.70, E.90, N.91, C.94, S.138, R.224 Ligands: NAG-NAG-BMA.5 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.224

1 x NAG- NAG- BMA- MAN- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(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-NAG.2: 10 residues within 4Å: Chain A: N.68, E.90, N.91, C.94, S.138, C.139, K.222, R.224, D.225 Ligands: NAG-NAG-BMA-MAN.1 No protein-ligand interaction detected (PLIP)

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.5: 5 residues within 4Å: Chain E: G.57, N.58, K.86 Ligands: NAG-NAG-BMA-MAN.6, NAG-NAG-BMA-MAN.6 No protein-ligand interaction detected (PLIP)

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

NAG.7: 1 residues within 4Å: Chain A: N.15 No protein-ligand interaction detected (PLIP) NAG.8: 3 residues within 4Å: Chain A: T.19, D.21, N.27 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.21 NAG.9: 3 residues within 4Å: Chain A: E.116, N.171, K.172 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.172 Water bridges: A:N.171 NAG.10: 1 residues within 4Å: Chain A: N.290 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.290 NAG.11: 2 residues within 4Å: Chain A: N.163, N.248 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.163, A:N.248 NAG.12: 1 residues within 4Å: Chain C: N.129 No protein-ligand interaction detected (PLIP) NAG.13: 2 residues within 4Å: Chain E: N.14, N.15 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.14 NAG.14: 2 residues within 4Å: Chain E: P.128, N.129 No protein-ligand interaction detected (PLIP) NAG.15: 1 residues within 4Å: Chain E: N.290 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.16: 2 residues within 4Å: Chain E: E.72, H.141 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:E.72, E:E.72, E:H.141

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Seok, J.H. et al., Divalent cation-induced conformational changes of influenza virus hemagglutinin. Sci Rep (2020)

Release Date

2020-10-21

Peptides

Hemagglutinin HA1 chain: ACE
Hemagglutinin HA2 chain: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
I

B
B

D
D

F
J

Hemagglutinin HA1 chain

Hemagglutinin HA2 chain

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