SMTL ID : 3s12.1

Crystal structure of H5N1 influenza virus hemagglutinin, strain YU562 crystal form 1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 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(Non-functional Binders)

NAG-NAG.1: 5 residues within 4Å: Chain A: N.178, N.249, D.250, A.251 Chain C: S.230 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain C: N.178, N.249, D.250, A.251 Chain E: S.230 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain A: S.230 Chain E: N.178, N.249, D.250, A.251 No protein-ligand interaction detected (PLIP)

6 x SO4: SULFATE ION(Non-functional Binders)(Post Translational Modification)

SO4.2: 3 residues within 4Å: Chain A: S.145, S.146, Q.235 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.146, A:Q.235 SO4.3: 5 residues within 4Å: Chain A: W.135, S.136, N.137, H.138, R.175 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.136, A:N.137, A:H.138 Salt bridges: A:H.138, A:R.175 SO4.6: 3 residues within 4Å: Chain C: S.145, S.146, Q.235 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.146, C:Q.235 SO4.7: 5 residues within 4Å: Chain C: W.135, S.136, N.137, H.138, R.175 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.136, C:N.137, C:H.138 Salt bridges: C:H.138, C:R.175 SO4.10: 3 residues within 4Å: Chain E: S.145, S.146, Q.235 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:S.146, E:Q.235 SO4.11: 5 residues within 4Å: Chain E: W.135, S.136, N.137, H.138, R.175 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:S.136, E:N.137, E:H.138 Salt bridges: E:H.138, E:R.175

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

NAG.4: 1 residues within 4Å: Chain A: N.36 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.36 NAG.8: 1 residues within 4Å: Chain C: N.36 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.36 NAG.12: 1 residues within 4Å: Chain E: N.36 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.36

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

DuBois, R.M. et al., Acid stability of the hemagglutinin protein regulates H5N1 influenza virus pathogenicity. Plos Pathog. (2011)

Release Date

2011-12-14

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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