SMTL ID : 6urm.1

Crystal structure of vaccine-elicited receptor-binding site targeting antibody LPAF-a.01 in complex with Hemagglutinin H1 A/California/04/2009

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

hetero-2-2-2-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 7 residues within 4Å: Chain B: K.45, A.46, E.48, W.49, N.62, L.65 Chain C: V.95 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.46, B:A.46

1 x NAG- NAG- MAN: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN.2: 7 residues within 4Å: Chain E: R.40, K.45, E.48, W.49, N.62, L.65 Chain F: V.95 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:R.40, E:K.45, E:K.45, E:E.48

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

NAG.3: 6 residues within 4Å: Chain A: N.64, P.65, N.87, C.90, C.136, P.137 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.65 Hydrogen bonds: A:N.64, A:N.87

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 4 residues within 4Å: Chain A: K.153, N.156 Chain C: P.54, S.55 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Y.48, C:S.55 Salt bridges: A:K.153 SO4.6: 2 residues within 4Å: Chain C: Q.184, H.188 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.184 Salt bridges: C:H.188 SO4.8: 7 residues within 4Å: Chain E: S.7, G.8, P.9, A.10, L.18, T.19, L.20 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.19 SO4.9: 3 residues within 4Å: Chain F: G.67, N.68, T.69 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:N.68, F:N.68, F:T.69

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: S.185, I.214 Chain B: T.31, S.32 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.32, B:S.32, A:S.185, A:I.214 GOL.7: 5 residues within 4Å: Chain A: K.208 Chain D: S.185, I.214 Chain E: T.31, S.32 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain D Hydrogen bonds: E:S.32, E:S.32, D:S.185, D:S.185, D:I.214

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cheung, C.S. et al., Identification and Structure of a Multidonor Class of Head-Directed Influenza-Neutralizing Antibodies Reveal the Mechanism for Its Recurrent Elicitation. Cell Rep (2020)

Release Date

2020-09-16

Peptides

Hemagglutinin: AD
The heavy chain of antibody LPAF-a.01: BE
The light chain of antibody LPAF-a.01: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

D
C

B
H

E
D

C
L

F
E

Hemagglutinin

The heavy chain of antibody LPAF-a.01

The light chain of antibody LPAF-a.01

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