SMTL ID : 6tvb.1

Crystal structure of the haemagglutinin from a transmissible H10N7 seal influenza virus isolated in Netherland in complex with human receptor analogue 6'-SLN

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

hetero-3-3-mer

Ligands

3 x NAG- GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-GAL-SIA.1: 12 residues within 4Å: Chain A: Y.90, G.127, T.128, T.129, K.130, W.146, V.148, H.178, E.185, L.189, L.221, G.223 11 PLIP interactions: 11 interactions with chain A Water bridges: A:S.181, A:Q.217, A:G.220, A:G.220, A:T.128, A:T.128, A:N.138, A:E.185, A:E.185, A:G.223 Hydrophobic interactions: A:W.146, A:V.148 Hydrogen bonds: A:T.128, A:K.130, A:H.178 NAG-GAL-SIA.2: 15 residues within 4Å: Chain C: Y.90, G.127, T.128, T.129, K.130, W.146, V.148, K.152, H.178, E.185, L.189, Q.217, G.220, L.221, G.223 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:Q.217, C:G.220, C:T.128, C:K.130, C:H.178 Salt bridges: C:K.152 Hydrophobic interactions: C:W.146, C:V.148 Water bridges: C:T.128, C:T.128, C:T.128, C:N.138, C:G.223 NAG-GAL-SIA.3: 12 residues within 4Å: Chain E: Y.90, G.127, T.128, T.129, K.130, W.146, H.178, S.181, E.185, L.189, L.221, G.223 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:S.181, E:S.181, E:E.185, E:Y.90, E:T.128, E:T.129, E:K.130, E:H.178 Water bridges: E:S.222, E:Q.217, E:T.128, E:T.128, E:N.138 Hydrophobic interactions: E:W.146

17 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 3 residues within 4Å: Chain A: H.179, F.208, V.209 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: R.134, S.139, F.140, A.142 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain B: E.132 Chain D: R.127, Q.128 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain C: P.234, D.236 Ligands: EDO.10 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: P.216, Q.217 Chain C: G.235, D.236, K.237 Ligands: EDO.9 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain C: A.166, D.167, P.234, G.235 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain C: D.1, P.2 Chain D: Y.141, H.142, N.169 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain C: H.10, T.29, N.30, T.313 Chain D: W.21 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain C: I.262, Q.263, W.278, R.295, T.296 Chain D: E.69 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain C: A.142, E.143, S.250, R.251 Ligand excluded by PLIP EDO.16: 2 residues within 4Å: Chain C: Y.119, G.120 Ligand excluded by PLIP EDO.17: 7 residues within 4Å: Chain A: V.212 Chain C: Q.158, S.196, S.198, S.241, H.242, N.243 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain D: R.25, H.26, T.32 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain E: P.288, K.302 Chain F: K.57, K.58 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain D: L.171 Chain F: E.164, L.167, L.168, L.171 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain F: H.26, G.33, Q.34, R.153 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain F: Y.141, H.142, A.143, N.169 Ligand excluded by PLIP

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

NAG.6: 5 residues within 4Å: Chain B: H.75, G.78, N.79, N.82 Chain C: E.106 No protein-ligand interaction detected (PLIP) NAG.7: 5 residues within 4Å: Chain B: S.147, E.150, S.151, N.154, T.156 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.150, B:E.150, B:N.154, B:T.156 NAG.18: 4 residues within 4Å: Chain D: H.75, N.79, N.82 Chain E: E.106 2 PLIP interactions: 2 interactions with chain D Water bridges: D:N.82, D: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

Hemagglutinin HA1: ACE
Hemagglutinin HA2: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

Hemagglutinin HA1

Hemagglutinin HA2