SMTL ID : 4cyz.1

Structure of the A_mallard_Sweden_51_2002 H10 Avian Haemmaglutinin in complex with avian receptor analog LSTA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-3-3-mer

Ligands

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

NAG-GAL-SIA.1: 11 residues within 4Å: Chain A: Y.88, G.125, T.126, T.127, K.128, W.144, H.176, E.183, L.187, Q.219, G.221 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Q.219, A:Q.219, A:T.126, A:K.128, A:H.176, A:E.183, A:Q.219, A:Q.219, A:G.221 Hydrophobic interactions: A:W.144 Water bridges: A:T.126

2 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(Non-functional Binders)

NAG-NAG-BMA-MAN-MAN.2: 8 residues within 4Å: Chain A: R.293 Chain B: H.75, N.79, N.82 Chain C: E.104, R.256 Chain D: E.64 Ligands: NAG.12 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:R.256, A:R.293 NAG-NAG-BMA-MAN-MAN.4: 7 residues within 4Å: Chain C: R.293 Chain D: H.75, G.78, N.79, N.82 Chain E: E.104, R.256 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.293

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: 4 residues within 4Å: Chain C: R.162, G.233, D.234, N.235 No protein-ligand interaction detected (PLIP)

1 x GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose(Non-covalent)

GAL-SIA.5: 13 residues within 4Å: Chain E: Y.88, G.125, T.126, T.127, K.128, N.136, W.144, V.146, H.176, E.183, L.187, Q.219, G.221 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:Q.219, E:Y.88, E:T.126, E:K.128, E:N.136, E:H.176, E:Q.219, E:Q.219 Hydrophobic interactions: E:W.144, E:V.146 Water bridges: E:T.126

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-functional Binders)

NAG-NAG-BMA-MAN.6: 9 residues within 4Å: Chain A: E.104, G.255, R.256 Chain E: R.293 Chain F: H.75, G.78, N.79, N.82 Ligands: EDO.23 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:R.256, E:R.293, A:G.255 Water bridges: E:R.293, A:R.256, A:R.256

6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-functional Binders)(Non-covalent)

NAG.7: 4 residues within 4Å: Chain A: R.162, G.233, D.234, N.235 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.162, A:G.233, A:N.235 NAG.8: 3 residues within 4Å: Chain A: N.28, A.29, T.30 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.28 NAG.12: 1 residues within 4Å: Ligands: NAG-NAG-BMA-MAN-MAN.2 No protein-ligand interaction detected (PLIP) NAG.13: 3 residues within 4Å: Chain B: E.150, N.154, T.156 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.154 NAG.15: 4 residues within 4Å: Chain C: N.28, T.30, T.311 Chain D: L.52 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:T.311, D:L.52 Hydrogen bonds: C:T.311 NAG.18: 3 residues within 4Å: Chain E: R.162, G.233, N.235 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.162

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

EDO.9: 7 residues within 4Å: Chain A: I.260, Q.261, W.276, R.277, R.293, T.294 Chain B: E.69 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.261, A:Q.261 Water bridges: A:R.277, B:S.65, B:S.65, B:S.65 EDO.10: 9 residues within 4Å: Chain A: Q.288, P.292, T.294, C.298, P.299, K.300, Y.301 Ligands: EDO.11, EDO.14 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.288, A:T.294, A:T.294, A:Y.301 Water bridges: A:Y.301, B:T.89 EDO.11: 6 residues within 4Å: Chain A: T.294, K.300 Chain B: F.63 Chain F: W.83 Ligands: EDO.10, EDO.14 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.294, A:K.300 Water bridges: A:P.292, A:T.294, A:K.300 EDO.14: 7 residues within 4Å: Chain A: P.292 Chain B: K.85, I.88, T.89 Chain F: W.83 Ligands: EDO.10, EDO.11 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:P.292, B:K.85, B:T.89, B:T.89 Water bridges: A:T.294, B:D.86 EDO.16: 5 residues within 4Å: Chain B: N.79 Chain C: Q.100, E.104 Chain D: E.64, S.65 8 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B, 4 interactions with chain D Hydrogen bonds: C:E.104, B:N.79, D:S.65, D:S.65 Water bridges: C:R.99, C:G.259, D:S.65, D:S.65 EDO.17: 7 residues within 4Å: Chain C: I.260, Q.261, W.276, R.277, R.293, V.295 Chain D: E.69 7 PLIP interactions: 2 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:Q.261, D:E.69, D:E.69 Water bridges: C:R.277, D:S.65, D:S.65, D:S.65 EDO.19: 6 residues within 4Å: Chain D: W.83 Chain E: T.294, C.298, K.300 Chain F: F.63 Ligands: EDO.22 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:T.294, E:K.300, E:K.300 Water bridges: E:T.294, E:T.294 EDO.20: 8 residues within 4Å: Chain E: L.60, L.170, I.171, M.172, P.247, R.249, V.250, S.251 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:L.60, E:M.172, E:S.251 EDO.21: 5 residues within 4Å: Chain E: T.63, P.64, A.65, I.84, C.87 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:A.65 EDO.22: 6 residues within 4Å: Chain D: W.83 Chain E: P.292 Chain F: K.85, I.88, T.89 Ligands: EDO.19 5 PLIP interactions: 1 interactions with chain F, 4 interactions with chain E Hydrogen bonds: F:T.89, E:P.292 Water bridges: E:Y.301, E:Y.301, E:Y.301 EDO.23: 3 residues within 4Å: Chain E: R.277 Chain F: E.69 Ligands: NAG-NAG-BMA-MAN.6 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:E.69, E:R.277, E:R.277

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vachieri, S.G. et al., Receptor Binding by H10 Influenza Viruses. Nature (2014)

Release Date

2014-06-11

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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