SMTL ID : 5xrs.2 (1 other biounit)

Crystal structure of A/Minnesota/11/2010 (H3N2) influenza virus hemagglutinin in complex with LSTc

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.91 Å

Oligo State

hetero-3-3-mer

Ligands

6 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 3 residues within 4Å: Chain A: N.38, A.39, T.318 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 4 residues within 4Å: Chain A: S.45, N.285, V.297, K.299 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 3 residues within 4Å: Chain C: N.38, A.39, T.318 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 4 residues within 4Å: Chain C: S.45, N.285, V.297, K.299 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 3 residues within 4Å: Chain E: N.38, A.39, T.318 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 4 residues within 4Å: Chain E: S.45, N.285, V.297, K.299 No protein-ligand interaction detected (PLIP)

3 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

NAG-NAG-BMA-MAN.2: 10 residues within 4Å: Chain A: E.163, Q.164, N.165, R.201, N.246, S.247, T.248 Chain E: D.188, I.217 Ligands: NAG-NAG-MAN-MAN-MAN.3 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:D.188, E:D.188 NAG-NAG-BMA-MAN.9: 10 residues within 4Å: Chain A: D.188, I.217 Chain C: E.163, Q.164, N.165, R.201, N.246, S.247, T.248 Ligands: NAG-NAG-MAN-MAN-MAN.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.188, A:D.188 NAG-NAG-BMA-MAN.16: 10 residues within 4Å: Chain C: D.188, I.217 Chain E: E.163, Q.164, N.165, R.201, N.246, S.247, T.248 Ligands: NAG-NAG-MAN-MAN-MAN.17 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.188

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

NAG-NAG-MAN-MAN-MAN.3: 7 residues within 4Å: Chain A: N.165, T.167 Chain E: S.219, P.221, W.222 Ligands: NAG-NAG-BMA-MAN.2, NAG-NAG-BMA-MAN.2 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:T.167 Hydrophobic interactions: E:W.222 NAG-NAG-MAN-MAN-MAN.10: 7 residues within 4Å: Chain A: S.219, P.221, W.222 Chain C: N.165, T.167 Ligands: NAG-NAG-BMA-MAN.9, NAG-NAG-BMA-MAN.9 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.222 NAG-NAG-MAN-MAN-MAN.17: 7 residues within 4Å: Chain C: S.219, P.221, W.222 Chain E: N.165, T.167 Ligands: NAG-NAG-BMA-MAN.16, NAG-NAG-BMA-MAN.16 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain E Hydrophobic interactions: C:W.222 Hydrogen bonds: E:T.167

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

NAG-NAG.5: 2 residues within 4Å: Chain A: K.62, N.63 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain C: K.62, N.63 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 2 residues within 4Å: Chain E: K.62, N.63 No protein-ligand interaction detected (PLIP)

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

BGC-GAL-NAG-GAL-SIA.6: 16 residues within 4Å: Chain A: Y.98, G.134, S.135, S.136, Y.137, N.145, W.153, Y.155, Y.159, H.183, D.190, N.193, L.194, G.225, V.226, S.228 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:N.193, A:L.194, A:Y.155 Hydrogen bonds: A:D.190, A:N.193, A:N.193, A:G.225, A:S.135, A:Y.137, A:N.145, A:H.183, A:S.228 BGC-GAL-NAG-GAL-SIA.13: 16 residues within 4Å: Chain C: Y.98, G.134, S.135, S.136, Y.137, N.145, W.153, Y.155, Y.159, H.183, D.190, N.193, L.194, G.225, V.226, S.228 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:N.193, C:L.194, C:Y.155 Hydrogen bonds: C:D.190, C:D.190, C:N.193, C:N.193, C:G.225, C:S.135, C:Y.137, C:N.145, C:H.183, C:S.228 BGC-GAL-NAG-GAL-SIA.20: 16 residues within 4Å: Chain E: Y.98, G.134, S.135, S.136, Y.137, N.145, W.153, Y.155, Y.159, H.183, D.190, N.193, L.194, G.225, V.226, S.228 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:N.193, E:L.194, E:Y.155 Hydrogen bonds: E:D.190, E:N.193, E:N.193, E:G.225, E:Y.98, E:S.135, E:Y.137, E:N.145, E:H.183, E:S.228

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

NAG.7: 2 residues within 4Å: Chain A: N.126, T.128 No protein-ligand interaction detected (PLIP) NAG.14: 2 residues within 4Å: Chain C: N.126, T.128 No protein-ligand interaction detected (PLIP) NAG.21: 2 residues within 4Å: Chain E: N.126, T.128 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bangaru, S. et al., A multifunctional human monoclonal neutralizing antibody that targets a unique conserved epitope on influenza HA. Nat Commun (2018)

Release Date

2018-07-25

Peptides

Hemagglutinin: ACE
Hemagglutinin: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

C
G

E
G

B
H

D
H

F
H

Hemagglutinin

Hemagglutinin

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