SMTL ID : 6wez.1

Crystal Structure of Broadly Neutralizing Antibody 3I14-D93N Mutant Bound to the Influenza A H3 Hemagglutinin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.21 Å

Oligo State

hetero-3-3-3-3-mer

Ligands

9 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.39, N.279, V.291, N.292 Chain B: E.69 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 11 residues within 4Å: Chain A: N.159, T.161, I.236 Chain I: T.181, S.213, R.214, P.215, R.216, N.219 Ligands: NAG-NAG-BMA.5, NAG-NAG-BMA.5 4 PLIP interactions: 3 interactions with chain I, 1 interactions with chain A Hydrophobic interactions: I:P.215, A:I.236 Hydrogen bonds: I:R.216, I:R.216 NAG-NAG-BMA.5: 9 residues within 4Å: Chain A: A.157, L.158, N.159, R.195, N.240, S.241, T.242 Chain I: I.211 Ligands: NAG-NAG-BMA.4 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 5 residues within 4Å: Chain E: N.39, N.279, V.291, N.292 Chain F: E.69 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 11 residues within 4Å: Chain A: T.181, S.213, R.214, P.215, R.216, N.219 Chain E: N.159, T.161, I.236 Ligands: NAG-NAG-BMA.12, NAG-NAG-BMA.12 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:P.215, E:I.236 Hydrogen bonds: A:R.216, A:R.216 NAG-NAG-BMA.12: 9 residues within 4Å: Chain A: I.211 Chain E: A.157, L.158, N.159, R.195, N.240, S.241, T.242 Ligands: NAG-NAG-BMA.11 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 5 residues within 4Å: Chain I: N.39, N.279, V.291, N.292 Chain J: E.69 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 11 residues within 4Å: Chain E: T.181, S.213, R.214, P.215, R.216, N.219 Chain I: N.159, T.161, I.236 Ligands: NAG-NAG-BMA.19, NAG-NAG-BMA.19 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain I Hydrophobic interactions: E:P.215, I:I.236 Hydrogen bonds: E:R.216, E:R.216 NAG-NAG-BMA.19: 9 residues within 4Å: Chain E: I.211 Chain I: A.157, L.158, N.159, R.195, N.240, S.241, T.242 Ligands: NAG-NAG-BMA.18 No protein-ligand interaction detected (PLIP)

9 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: 4 residues within 4Å: Chain A: N.32, A.33, T.34 Chain C: F.109 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: Q.126, N.127 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: E.56, N.57, Y.88 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain E: N.32, A.33, T.34 Chain G: F.109 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain E: Q.126, N.127 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain E: E.56, N.57, Y.88 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain I: N.32, A.33, T.34 Chain K: F.109 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 2 residues within 4Å: Chain I: Q.126, N.127 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 3 residues within 4Å: Chain I: E.56, N.57, Y.88 No protein-ligand interaction detected (PLIP)

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 2 residues within 4Å: Chain A: R.301 Chain J: Y.94 No protein-ligand interaction detected (PLIP) GOL.14: 2 residues within 4Å: Chain B: Y.94 Chain E: R.301 No protein-ligand interaction detected (PLIP) GOL.21: 2 residues within 4Å: Chain F: Y.94 Chain I: R.301 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Harshbarger, W.D. et al., Unique structural solution from a V H 3-30 antibody targeting the hemagglutinin stem of influenza A viruses. Nat Commun (2021)

Release Date

2020-11-25

Peptides

Hemagglutinin: AEI
Hemagglutinin: BFJ
heavy chain: CGK
light chain: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
A

I
A

B
B

F
B

J
B

C
H

G
H

K
H

D
L

H
L

L
L

Hemagglutinin

Hemagglutinin

heavy chain

light chain

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