SMTL ID : 6tva.1

Crystal structure of the haemagglutinin from a transmissible H10N7 seal influenza virus isolated in Netherland in complex with avian receptor analogue, 3'-SLN

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

hetero-3-3-mer

Ligands

3 x NAG- GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-GAL-SIA.1: 17 residues within 4Å: Chain A: Y.90, G.127, T.128, T.129, K.130, N.138, W.146, V.148, H.178, S.181, E.185, L.189, Q.217, G.220, L.221, S.222, G.223 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:K.130, A:K.130, A:S.181, A:Q.217, A:S.222, A:S.222, A:G.223, A:Y.90, A:T.128, A:T.129, A:K.130, A:N.138, A:H.178 Hydrophobic interactions: A:W.146, A:V.148 Water bridges: A:T.128, A:T.128 NAG-GAL-SIA.2: 15 residues within 4Å: Chain C: Y.90, G.127, T.128, T.129, K.130, W.146, V.148, H.178, S.181, E.185, L.189, Q.217, G.220, L.221, G.223 9 PLIP interactions: 9 interactions with chain C Water bridges: C:E.185, C:E.185, C:T.128, C:T.128, C:N.138, C:S.181 Hydrogen bonds: C:S.181, C:S.181, C:Q.217, C:T.128, C:K.130, C:H.178 Hydrophobic interactions: C:W.146, C:V.148 NAG-GAL-SIA.4: 16 residues within 4Å: Chain E: Y.90, G.127, T.128, T.129, K.130, W.146, V.148, H.178, S.181, E.185, L.189, Q.217, G.220, L.221, S.222, G.223 12 PLIP interactions: 12 interactions with chain E Water bridges: E:E.185, E:E.185, E:E.185, E:E.185, E:S.222, E:G.223, E:T.128, E:T.128, E:T.128, E:S.181, E:E.185, E:G.223 Hydrogen bonds: E:S.181, E:Q.217, E:S.222, E:S.222, E:T.128, E:K.130, E:N.138, E:H.178 Hydrophobic interactions: E:W.146, E:V.148

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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: 5 residues within 4Å: Chain D: S.147, E.150, S.151, N.154, T.156 No protein-ligand interaction detected (PLIP)

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

NAG.5: 1 residues within 4Å: Chain A: N.30 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.30 NAG.6: 5 residues within 4Å: Chain A: R.295 Chain B: H.75, N.79, N.82 Chain C: E.106 2 PLIP interactions: 2 interactions with chain B Water bridges: B:N.82, B:N.82 NAG.7: 5 residues within 4Å: Chain D: H.75, G.78, N.79, N.82 Chain E: E.106 2 PLIP interactions: 2 interactions with chain D Water bridges: D:N.82, D:N.82 NAG.8: 1 residues within 4Å: Chain E: N.30 1 PLIP interactions: 1 interactions with chain E Water bridges: E:T.313 NAG.9: 4 residues within 4Å: Chain A: E.106 Chain F: H.75, N.79, N.82 2 PLIP interactions: 2 interactions with chain F Water bridges: F:N.82, F:N.82

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Herfst, S. et al., Hemagglutinin Traits Determine Transmission of Avian A/H10N7 Influenza Virus between Mammals. Cell Host Microbe (2020)

Release Date

2020-10-21

Peptides

Haemagglutinin HA1: ACE
Haemagglutinin HA2: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

Haemagglutinin HA1

Haemagglutinin HA2

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