SMTL ID : 4o5i.1 (1 other biounit)

Crystal structure of broadly neutralizing antibody F045-092 in complex with A/Victoria/361/2011 (H3N2) influenza hemagglutinin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 6.50 Å

Oligo State

hetero-3-3-3-3-mer

Ligands

5 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: 5 residues within 4Å: Chain A: N.32, T.312 Chain B: N.49, L.52, I.56 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.52 NAG-NAG-BMA.11: 4 residues within 4Å: Chain C: N.279, V.291, N.292 Chain D: E.69 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:E.69 NAG-NAG-BMA.12: 9 residues within 4Å: Chain A: D.182, N.210, I.211 Chain C: A.157, L.158, R.195, T.197, N.240, T.242 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 4 residues within 4Å: Chain E: E.56, N.57, K.86, Y.88 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 8 residues within 4Å: Chain C: D.182, I.211 Chain E: A.157, L.158, R.195, T.197, N.240 Ligands: NAG-NAG-BMA-MAN-MAN.16 No protein-ligand interaction detected (PLIP)

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.2: 3 residues within 4Å: Chain A: E.56, N.57, Y.88 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: Q.126, N.127, R.249 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: N.39, N.279, V.291, N.292 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain A: A.157, L.158, R.195, N.240, T.242 Chain E: I.211 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain C: E.56, N.57, Y.88 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain E: N.39, N.279, V.291, N.292 No protein-ligand interaction detected (PLIP)

4 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.4: 3 residues within 4Å: Chain A: N.159 Chain E: S.213, R.216 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.10: 3 residues within 4Å: Chain A: S.213, R.216 Chain C: N.159 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.13: 4 residues within 4Å: Chain E: N.32, T.34, T.312 Chain F: I.56 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.16: 5 residues within 4Å: Chain C: S.213, R.216 Chain E: N.159, N.240 Ligands: NAG-NAG-BMA.18 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.7: 4 residues within 4Å: Chain C: N.32, T.312 Chain D: L.52, I.56 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.52, D:I.56 NAG-NAG-BMA-MAN.9: 4 residues within 4Å: Chain C: Q.126, N.127, R.249 Chain I: S.103 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.15: 3 residues within 4Å: Chain E: Q.126, N.127, R.249 No protein-ligand interaction detected (PLIP)

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

NAG.19: 1 residues within 4Å: Chain B: N.154 No protein-ligand interaction detected (PLIP) NAG.20: 2 residues within 4Å: Chain C: N.120, T.122 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.120, C:T.122 NAG.21: 1 residues within 4Å: Chain D: N.154 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.154 NAG.22: 2 residues within 4Å: Chain E: N.120, T.122 No protein-ligand interaction detected (PLIP) NAG.23: 1 residues within 4Å: Chain F: N.154 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, P.S. et al., Receptor mimicry by antibody F045-092 facilitates universal binding to the H3 subtype of influenza virus. Nat Commun (2014)

Release Date

2014-04-16

Peptides

Hemagglutinin HA1 chain: ACE
Hemagglutinin HA2 chain: BDF
Fab F045-092 heavy chain: GIK
Fab F045-092 light chain: HJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

G
M

I
O

K
Q

H
N

J
P

L
R

Hemagglutinin HA1 chain

Hemagglutinin HA2 chain

Fab F045-092 heavy chain

Fab F045-092 light chain

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