SMTL ID : 6tjw.1

Crystal structure of the haemagglutinin mutant (Gln226Leu, Del228) from an H10N7 seal influenza virus isolated in Germany

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

hetero-3-3-mer

Ligands

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.1: 8 residues within 4Å: Chain A: R.294 Chain B: H.75, G.78, N.79, N.82 Chain C: E.106, R.257 Ligands: CA.3 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.257

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

NAG.2: 3 residues within 4Å: Chain A: N.30, T.312 Chain B: L.52 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.312 Water bridges: A:N.30, A:T.312 Hydrophobic interactions: B:L.52 NAG.4: 3 residues within 4Å: Chain C: N.30, A.31, T.32 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.32, C:T.32 Water bridges: C:E.33 NAG.7: 2 residues within 4Å: Chain D: N.79, N.82 3 PLIP interactions: 3 interactions with chain D Water bridges: D:G.78, D:N.79, D:N.79 NAG.8: 4 residues within 4Å: Chain E: N.30, T.32, T.312 Chain F: L.52 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.30, E:T.312 NAG.10: 6 residues within 4Å: Chain A: E.106, R.257 Chain F: H.75, G.78, N.79, N.82 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain A Water bridges: F:N.82 Hydrogen bonds: A:R.257

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain B: N.79 Chain C: E.106, R.257 Chain D: E.64 Ligands: NAG-NAG.1 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: C:E.106, D:E.64, H2O.22

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

EDO.5: 5 residues within 4Å: Chain C: K.19, K.305, S.307, L.308, M.309 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:K.19, C:K.305, C:K.305, C:M.309 Water bridges: C:K.19, C:M.309 EDO.6: 6 residues within 4Å: Chain B: Y.94 Chain C: P.287, F.288, K.301 Chain D: K.57, K.58 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:P.287, C:K.301 Water bridges: D:T.59 EDO.9: 4 residues within 4Å: Chain D: Y.94 Chain E: P.287, K.301 Chain F: K.57 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:P.287, E:K.301 Water bridges: F:T.59 EDO.11: 4 residues within 4Å: Chain D: Y.94, E.97, L.98 Chain F: R.54 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain D Hydrogen bonds: F:R.54, D:Y.94, D:Y.94

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

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