SMTL ID : 5xrt.1 (1 other biounit)

Crystal structure of A/Minnesota/11/2010 (H3N2) influenza virus hemagglutinin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.15 Å

Oligo State

hetero-3-3-mer

Ligands

1 x NAG- NAG- BMA- FUL- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-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:N.38

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: 4 residues within 4Å: Chain A: N.38, T.318 Chain B: L.52 Ligands: NAG-NAG-BMA-FUL-FUC.1 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.3: 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-MAN.4 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.188 NAG-NAG-BMA-MAN.8: 12 residues within 4Å: Chain A: D.188, I.217, G.218 Chain C: E.163, Q.164, N.165, R.201, I.203, N.246, S.247, T.248 Ligands: NAG-NAG-MAN-MAN-MAN-MAN.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.188, A:D.188, A:D.188

3 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: 9 residues within 4Å: Chain A: N.165, T.167, L.244 Chain E: Y.137, S.219, P.221, W.222 Ligands: NAG-NAG-BMA-MAN.3, NAG-NAG-BMA-MAN.3 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-MAN.9: 7 residues within 4Å: Chain A: S.219, P.221, W.222 Chain C: N.165, T.167, L.244 Ligands: NAG-NAG-BMA-MAN.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.222 NAG-NAG-MAN-MAN-MAN-MAN.15: 5 residues within 4Å: Chain C: S.219, P.221, W.222 Chain E: N.165 Ligands: NAG-NAG-BMA-MAN-MAN.14 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:W.222

3 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.5: 5 residues within 4Å: Chain A: N.285, V.297, N.298 Chain B: E.69 Chain C: S.262 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.262 NAG-NAG-BMA-MAN-MAN.13: 4 residues within 4Å: Chain E: N.38, T.318 Chain F: L.52 Ligands: NAG-FUL-FUC.12 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.16: 5 residues within 4Å: Chain E: S.45, N.285, N.296, V.297 Chain F: E.69 No protein-ligand interaction detected (PLIP)

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.6: 1 residues within 4Å: Chain A: N.63 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain C: N.63, Y.94 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 2 residues within 4Å: Chain E: N.63, Y.94 No protein-ligand interaction detected (PLIP)

2 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.7: 1 residues within 4Å: Chain C: N.38 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 3 residues within 4Å: Chain C: N.285, V.297 Chain D: E.69 No protein-ligand interaction detected (PLIP)

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.12: 4 residues within 4Å: Chain E: N.22, T.24, N.38 Ligands: NAG-NAG-BMA-MAN-MAN.13 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-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-MAN.14: 12 residues within 4Å: Chain C: D.188, I.217, S.219 Chain E: E.163, Q.164, N.165, R.201, N.246, S.247, T.248 Ligands: NAG-NAG-MAN-MAN-MAN-MAN.15, NAG-NAG-FUC.17 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.188, C:D.188

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.17: 6 residues within 4Å: Chain E: N.126, T.128, P.162, E.163 Ligands: NAG-NAG-BMA-MAN-MAN.14, NAG-NAG-BMA-MAN-MAN.14 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:P.162

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

NAG.19: 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.20: 2 residues within 4Å: Chain B: G.150, N.154 No protein-ligand interaction detected (PLIP) NAG.22: 2 residues within 4Å: Chain C: N.126, T.128 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:N.126 NAG.23: 2 residues within 4Å: Chain D: N.154, T.156 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.147, D:N.154 NAG.24: 2 residues within 4Å: Chain F: G.150, N.154 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.154

1 x CAC: CACODYLATE ION(Non-covalent)

CAC.21: 4 residues within 4Å: Chain B: E.128 Chain D: E.128 Chain F: E.128, R.170 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:E.128

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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