SMTL ID : 4ln8.1 (7 other biounits)

The crystal structure of hemagglutinin from a h7n9 influenza virus (a/shanghai/2/2013) in complex with lstb

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-3-3-mer

Ligands

3 x NAG- NAG- BMA- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG-BMA-FUC.1: 3 residues within 4Å: Chain A: N.16, T.18, N.32 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.4: 4 residues within 4Å: Chain C: N.16, T.18, N.32 Ligands: NAG-NAG-BMA.5 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.7: 3 residues within 4Å: Chain E: N.16, T.18, N.32 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: 4 residues within 4Å: Chain A: N.32, T.34, T.313 Chain B: L.52 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 4 residues within 4Å: Chain C: N.32, T.34, T.313 Ligands: NAG-NAG-BMA-FUC.4 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 4 residues within 4Å: Chain E: N.32, T.34, T.313 Chain F: L.52 No protein-ligand interaction detected (PLIP)

1 x GAL- NAG- GAL- SIA: beta-D-galactopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-6)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose

GAL-NAG-GAL-SIA.3: 12 residues within 4Å: Chain A: Y.92, A.129, T.130, S.131, W.146, L.148, H.178, V.181, E.185, L.189, N.219, L.221 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.185, A:Y.92, A:A.129, A:T.130, A:S.131, A:H.178 Hydrophobic interactions: A:L.189 Water bridges: A:A.129, A:A.129

1 x NAG- GAL- SIA: beta-D-galactopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-GAL-SIA.6: 13 residues within 4Å: Chain C: Y.92, A.129, T.130, S.131, W.146, L.148, H.178, V.181, E.185, K.188, L.189, L.221, G.223 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:E.185, C:E.185, C:Y.92, C:A.129, C:T.130, C:S.131, C:H.178 Hydrophobic interactions: C:L.189 Water bridges: C:A.129, C:A.129

1 x NAG- SIA: N-acetyl-alpha-neuraminic acid-(2-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-SIA.9: 11 residues within 4Å: Chain E: Y.92, A.129, T.130, S.131, W.146, L.148, H.178, E.185, L.189, L.221, G.223 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:L.189 Hydrogen bonds: E:A.129, E:T.130, E:S.131, E:H.178 Water bridges: E:A.129, E:A.129

3 x CA: CALCIUM ION(Non-covalent)

CA.10: 3 residues within 4Å: Chain A: E.75, D.113, K.114 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.75, A:D.113, A:K.114 CA.12: 3 residues within 4Å: Chain C: E.75, D.113, K.114 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.75, C:D.113, C:K.114 CA.14: 3 residues within 4Å: Chain E: E.75, D.113, K.114 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:E.75, E:D.113, E:K.114

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

NAG.11: 5 residues within 4Å: Chain B: E.72, K.75, N.79, N.82 Chain C: E.108 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:K.75 NAG.13: 3 residues within 4Å: Chain D: N.79, N.82 Chain E: E.108 No protein-ligand interaction detected (PLIP) NAG.15: 3 residues within 4Å: Chain A: E.108 Chain F: N.79, N.82 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, H. et al., Structural Analysis of the Hemagglutinin from the Recent 2013 H7N9 Influenza Virus. J.Virol. (2013)

Release Date

2013-10-02

Peptides

Hemagglutinin: ACE
Hemagglutinin: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

Hemagglutinin

Hemagglutinin

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