SMTL ID : 6fyw.1

Structure of B/Brisbane/60/2008 Influenza Hemagglutinin in complex with SD83

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-3-3-3-mer

Ligands

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.1: 1 residues within 4Å: Chain A: N.233 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.11: 1 residues within 4Å: Chain D: N.233 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.21: 1 residues within 4Å: Chain G: N.233 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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-MAN-MAN.2: 9 residues within 4Å: Chain A: K.45, G.291, E.292, G.302, N.304 Chain C: G.55, S.56, W.57, G.66 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.292 Hydrogen bonds: A:E.292 NAG-NAG-BMA-MAN-MAN-MAN-MAN.12: 9 residues within 4Å: Chain D: K.45, G.291, E.292, G.302, N.304 Chain F: G.55, S.56, W.57, G.66 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:E.292 Hydrogen bonds: D:E.292 NAG-NAG-BMA-MAN-MAN-MAN-MAN.22: 9 residues within 4Å: Chain G: K.45, G.291, E.292, G.302, N.304 Chain I: G.55, S.56, W.57, G.66 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:E.292 Hydrogen bonds: G:E.292

6 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 A: N.197, T.199, Q.200, S.243 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.145, I.146, G.149, N.150 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain D: N.197, T.199, Q.200, S.243 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain D: N.145, I.146, G.149, N.150 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain G: N.197, T.199, Q.200, S.243 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 4 residues within 4Å: Chain G: N.145, I.146, G.149, N.150 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-2)-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.5: 9 residues within 4Å: Chain A: I.30, N.333 Chain B: W.21, T.41, I.45 Chain C: Q.39, R.45, R.114, L.115 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:Q.39, C:Q.39, C:R.114 Hydrophobic interactions: B:W.21, B:T.41, B:I.45 NAG-NAG-BMA-MAN-MAN.15: 9 residues within 4Å: Chain D: I.30, N.333 Chain E: W.21, T.41, I.45 Chain F: Q.39, R.45, R.114, L.115 4 PLIP interactions: 1 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:Q.39, F:Q.39, F:R.114 Hydrophobic interactions: E:W.21, E:T.41, E:I.45 NAG-NAG-BMA-MAN-MAN.25: 9 residues within 4Å: Chain G: I.30, N.333 Chain H: W.21, T.41, I.45 Chain I: Q.39, R.45, R.114, L.115 4 PLIP interactions: 1 interactions with chain I, 3 interactions with chain H Hydrogen bonds: I:Q.39, I:Q.39, I:R.114 Hydrophobic interactions: H:W.21, H:T.41, H:I.45

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

NAG.6: 3 residues within 4Å: Chain A: P.13, E.23, N.25 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.23 Hydrogen bonds: A:N.25 NAG.16: 3 residues within 4Å: Chain D: P.13, E.23, N.25 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:E.23 Hydrogen bonds: D:N.25 NAG.26: 3 residues within 4Å: Chain G: P.13, E.23, N.25 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:E.23 Hydrogen bonds: G:N.25

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 8 residues within 4Å: Chain A: G.184, E.185, D.186, K.254, A.276, S.277, G.278 Ligands: GOL.9 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.186, A:D.186, A:K.254, A:K.254, A:G.278 GOL.8: 3 residues within 4Å: Chain A: G.138, T.139, W.158 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.139 Water bridges: A:T.139 GOL.9: 7 residues within 4Å: Chain A: G.113, Y.114, G.278, R.279 Chain B: S.67, G.68 Ligands: GOL.7 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain B, 1 interactions with chain A Water bridges: E:E.79 Hydrogen bonds: B:S.67, A:G.113 GOL.10: 5 residues within 4Å: Chain A: H.314, W.324 Chain B: D.86, D.90 Chain H: K.61 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain H Hydrogen bonds: B:D.90, H:K.61 GOL.17: 8 residues within 4Å: Chain D: G.184, E.185, D.186, K.254, A.276, S.277, G.278 Ligands: GOL.19 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.186, D:D.186, D:K.254, D:K.254, D:G.278 GOL.18: 3 residues within 4Å: Chain D: G.138, T.139, W.158 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.139 Water bridges: D:T.139 GOL.19: 7 residues within 4Å: Chain D: G.113, Y.114, G.278, R.279 Chain E: S.67, G.68 Ligands: GOL.17 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E, 1 interactions with chain H Hydrogen bonds: D:G.113, E:S.67 Water bridges: H:E.79 GOL.20: 5 residues within 4Å: Chain B: K.61 Chain D: H.314, W.324 Chain E: D.86, D.90 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain B Hydrogen bonds: E:D.86, E:D.90, E:D.90, B:K.61 GOL.27: 8 residues within 4Å: Chain G: G.184, E.185, D.186, K.254, A.276, S.277, G.278 Ligands: GOL.29 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:D.186, G:D.186, G:K.254, G:K.254, G:G.278 GOL.28: 3 residues within 4Å: Chain G: G.138, T.139, W.158 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:T.139 GOL.29: 7 residues within 4Å: Chain G: G.113, Y.114, G.278, R.279 Chain H: S.67, G.68 Ligands: GOL.27 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain H, 2 interactions with chain G Water bridges: B:E.79, G:D.186 Hydrogen bonds: H:S.67, G:G.113 GOL.30: 5 residues within 4Å: Chain E: K.61 Chain G: H.314, W.324 Chain H: D.86, D.90 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain H Hydrogen bonds: E:K.61, H:D.90, H:D.90

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Laursen, N.S. et al., Universal protection against influenza infection by a multidomain antibody to influenza hemagglutinin. Science (2018)

Release Date

2018-11-07

Peptides

Hemagglutinin: ADG
Hemagglutinin: BEH
Single domain antibody SD83: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

G
A

B
B

E
B

H
B

C
C

F
C

I
C

Hemagglutinin

Hemagglutinin

Single domain antibody SD83

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