SMTL ID : 4fqr.2 (3 other biounits)

Crystal structure of broadly neutralizing antibody C05 bound to H3 influenza hemagglutinin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 4.10 Å

Oligo State

hetero-3-3-3-3-mer

Ligands

3 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.1: 4 residues within 4Å: Chain A: N.159, T.161 Chain C: P.215, W.216 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:W.216 NAG-NAG-BMA-MAN.3: 6 residues within 4Å: Chain C: N.159, T.161, V.236 Chain E: S.213, P.215, W.216 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:W.216 Hydrophobic interactions: C:V.236 NAG-NAG-BMA-MAN.5: 4 residues within 4Å: Chain A: P.215, W.216 Chain E: N.159, T.161 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.216

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.2: 5 residues within 4Å: Chain A: S.39, N.279, V.291, N.292 Chain B: E.69 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain C: S.39, N.279, V.291, N.292, K.293 Chain D: E.69 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain E: S.39, N.279, V.291, N.292, K.293 Chain F: E.69 No protein-ligand interaction detected (PLIP)

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

NAG.7: 3 residues within 4Å: Chain A: N.32, T.312 Chain B: L.52 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.32, A:T.312 NAG.8: 3 residues within 4Å: Chain A: N.75, E.113, F.114 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.75, A:E.113, A:E.113 NAG.9: 5 residues within 4Å: Chain B: A.147, E.150, S.151, N.154, T.156 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.147 NAG.10: 3 residues within 4Å: Chain C: N.32, T.312 Chain D: L.52 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.32, C:T.312 NAG.11: 5 residues within 4Å: Chain D: A.147, E.150, S.151, N.154, T.156 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:A.147 NAG.12: 4 residues within 4Å: Chain E: N.75, E.113, F.114, I.115 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.75, E:E.113, E:F.114 NAG.13: 5 residues within 4Å: Chain F: A.147, E.150, S.151, N.154, T.156 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:A.147

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ekiert, D.C. et al., Cross-neutralization of influenza A viruses mediated by a single antibody loop. Nature (2012)

Release Date

2012-09-19

Peptides

Hemagglutinin HA1 chain: ACE
Hemagglutinin HA2 chain: BDF
Broadly neutralizing antibody C05, heavy chain: GIK
Broadly neutralizing antibody C05, light chain: HJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

C
I

E
K

B
H

D
J

F
L

G
g

I
i

K
k

H
h

J
j

L
l

Hemagglutinin HA1 chain

Hemagglutinin HA2 chain

Broadly neutralizing antibody C05, heavy chain

Broadly neutralizing antibody C05, light chain

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