SMTL ID : 6twi.1

Crystal structure of the haemagglutinin mutant (Gln226Leu, Gly228Ser) from an H10N7 seal influenza virus isolated in Germany in complex with avian receptor analogue 3'-SLN

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.27 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: 14 residues within 4Å: Chain A: Y.90, G.127, T.128, T.129, K.130, W.146, H.178, S.181, E.185, L.189, G.220, L.221, S.222, S.223 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.181, A:S.181, A:Q.217, A:Y.90, A:T.128, A:T.129, A:K.130, A:H.178, A:S.223 Water bridges: A:S.222, A:T.128, A:S.181 Hydrophobic interactions: A:W.146 NAG-GAL-SIA.2: 16 residues within 4Å: Chain C: Y.90, G.127, T.128, T.129, K.130, N.138, W.146, H.178, S.181, E.185, L.189, Q.217, N.219, G.220, L.221, S.223 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:S.181, C:S.181, C:Q.217, C:Y.90, C:T.128, C:T.129, C:K.130, C:N.138, C:S.223, C:S.223 Water bridges: C:S.222, C:S.222, C:T.128, C:T.128, C:T.128, C:S.181 Hydrophobic interactions: C:W.146 NAG-GAL-SIA.4: 11 residues within 4Å: Chain E: Y.90, G.127, T.128, T.129, K.130, W.146, H.178, E.185, L.189, L.221, S.223 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:K.130, E:T.128, E:K.130, E:H.178, E:S.223 Hydrophobic interactions: E:W.146 Water bridges: E:T.128, E:N.138

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.3: 8 residues within 4Å: Chain A: E.106, R.258 Chain C: R.295 Chain D: H.75, G.78, N.79, N.82 Ligands: CA.8 No protein-ligand interaction detected (PLIP)

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

NAG.5: 3 residues within 4Å: Chain A: N.30, T.32, T.313 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.32, A:T.313 Water bridges: A:N.30 NAG.9: 6 residues within 4Å: Chain B: H.75, G.78, N.79, N.82 Chain E: E.106 Ligands: CA.15 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.82 NAG.11: 3 residues within 4Å: Chain C: N.30, T.313 Chain D: L.52 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.313 Water bridges: C:N.30 NAG.14: 2 residues within 4Å: Chain E: N.30, T.313 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.30 Water bridges: E:T.313, E:T.313 NAG.16: 6 residues within 4Å: Chain C: E.106 Chain F: H.75, G.78, N.79, N.82 Ligands: CA.13 1 PLIP interactions: 1 interactions with chain C Water bridges: C:R.258

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

EDO.6: 8 residues within 4Å: Chain A: M.105, E.106, G.259, L.260, G.261, V.297 Chain B: E.64, S.65 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.65, A:M.105, A:G.261 EDO.7: 7 residues within 4Å: Chain A: I.262, Q.263, W.278, R.295, T.296, V.297 Chain B: E.69 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.263, A:Q.263, A:R.295 Water bridges: A:R.279 EDO.10: 3 residues within 4Å: Chain A: K.83, R.279 Chain B: E.69 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.279 EDO.12: 9 residues within 4Å: Chain A: S.198, V.199, G.200, K.205, N.206 Chain C: V.211, G.213, A.214, R.215 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.214, C:R.215

3 x CA: CALCIUM ION(Non-covalent)

CA.8: 4 residues within 4Å: Chain A: E.106 Chain B: E.64 Chain D: N.79 Ligands: NAG-NAG.3 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:E.106, B:E.64, H2O.15 CA.13: 5 residues within 4Å: Chain C: E.106, R.258 Chain D: E.64 Chain F: N.79 Ligands: NAG.16 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.64, H2O.9, H2O.15 CA.15: 4 residues within 4Å: Chain B: N.79 Chain E: E.106 Chain F: E.64 Ligands: NAG.9 4 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: E:E.106, F:E.64, H2O.7, H2O.19

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: 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

Hemagglutinin HA2

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