SMTL ID : 5xrs.1 (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

1 x NAG- FUL- FUC: beta-L-fucopyranose-(1-3)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-FUL-FUC.1: 6 residues within 4Å: Chain A: N.22, T.24, T.37, N.38, A.39 Ligands: NAG-NAG-BMA-MAN.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.39 Hydrophobic interactions: A:T.24

2 x NAG- NAG- BMA- MAN: 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

NAG-NAG-BMA-MAN.2: 4 residues within 4Å: Chain A: N.38, T.318 Chain B: L.52 Ligands: NAG-FUL-FUC.1 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.5: 5 residues within 4Å: Chain A: N.285, V.297, N.298 Chain B: E.69 Chain E: S.262 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.262

4 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.3: 9 residues within 4Å: Chain A: E.163, N.165, R.201, N.246, S.247, T.248 Chain C: D.188, I.217 Ligands: NAG-NAG-MAN-MAN-MAN-MAN.4 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.188, C:D.188 NAG-NAG-BMA-MAN.9: 4 residues within 4Å: Chain C: N.38, T.318 Chain D: L.52 Ligands: NAG-FUL.8 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.10: 9 residues within 4Å: Chain C: E.163, N.165, R.201, N.246, S.247, T.248 Chain E: D.188, I.217 Ligands: NAG-NAG-MAN-MAN-MAN-MAN-MAN.11 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.188 NAG-NAG-BMA-MAN.15: 3 residues within 4Å: Chain E: N.38, T.318 Chain F: L.52 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN.4: 6 residues within 4Å: Chain A: N.165, L.244 Chain C: Y.137, S.219, W.222 Ligands: NAG-NAG-BMA-MAN.3 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.222

1 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.6: 1 residues within 4Å: Chain A: N.63 No protein-ligand interaction detected (PLIP)

2 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.7: 18 residues within 4Å: Chain A: Y.98, G.134, S.135, S.136, Y.137, N.145, W.153, Y.155, Y.159, N.193, L.194, W.222, G.225, V.226, S.227, S.228 Ligands: NAG-NAG-BMA-MAN-MAN.16, NAG-NAG-BMA-MAN-MAN.16 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.194, A:Y.155, A:L.194 Hydrogen bonds: A:N.193, A:G.225, A:S.135, A:Y.137, A:N.145, A:S.228 BGC-GAL-NAG-GAL-SIA.14: 16 residues within 4Å: Chain C: Y.98, G.134, S.135, S.136, Y.137, W.153, Y.155, Y.159, H.183, K.189, D.190, N.193, L.194, G.225, V.226, S.228 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:N.193, C:L.194, C:W.153, C:Y.155, C:L.194 Hydrogen bonds: C:T.192, C:G.225, C:S.135, C:Y.137, C:S.228, C:S.228

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

NAG-FUL.8: 8 residues within 4Å: Chain C: N.22, G.23, T.24, T.37, N.38, A.39 Ligands: NAG-NAG-BMA-MAN.9, NAG-NAG-BMA-MAN.9 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.38, C:N.22 Hydrophobic interactions: C:T.24

1 x NAG- NAG- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]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-MAN-MAN.11: 6 residues within 4Å: Chain C: N.165, T.167 Chain E: S.219, P.221, W.222 Ligands: NAG-NAG-BMA-MAN.10 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:W.222

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

NAG-NAG-BMA-MAN-MAN.12: 5 residues within 4Å: Chain C: S.45, N.285, V.297, N.298 Chain D: E.69 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.16: 11 residues within 4Å: Chain A: S.219, P.221, W.222 Chain E: E.163, N.165, T.167, L.244, N.246 Ligands: BGC-GAL-NAG-GAL-SIA.7, NAG-NAG.17, NAG-NAG.17 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:W.222, A:W.222 Hydrophobic interactions: E:L.244

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

NAG-NAG.13: 2 residues within 4Å: Chain C: N.63, Y.94 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 5 residues within 4Å: Chain E: N.165, V.166, T.167 Ligands: NAG-NAG-BMA-MAN-MAN.16, NAG-NAG-BMA-MAN-MAN.16 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain E: S.45, N.285, V.297 Chain F: E.69 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 2 residues within 4Å: Chain E: N.63, T.92 No protein-ligand interaction detected (PLIP)

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

NAG.20: 2 residues within 4Å: Chain A: N.126, T.128 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.126, A:T.128 NAG.21: 5 residues within 4Å: Chain B: A.147, G.150, S.151, N.154, T.156 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.147 NAG.22: 2 residues within 4Å: Chain C: N.126, T.128 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.126 NAG.24: 3 residues within 4Å: Chain D: A.147, G.150, N.154 No protein-ligand interaction detected (PLIP) NAG.25: 2 residues within 4Å: Chain E: N.126, T.128 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.126 NAG.26: 3 residues within 4Å: Chain F: A.147, G.150, N.154 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:A.147, F:N.154

1 x CAC: CACODYLATE ION(Non-covalent)

CAC.23: 6 residues within 4Å: Chain B: E.128, R.170 Chain D: E.128, R.170 Chain F: E.128, R.170 3 PLIP interactions: 1 interactions with chain F, 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: F:R.170, D:E.128, B:R.170

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
A

C
C

E
E

B
B

D
D

F
F

Hemagglutinin

Hemagglutinin

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