SMTL ID : 6e3h.1

Crystal structure of S9-3-37 bound to H5 influenza hemagglutinin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-3-3-3-3-mer

Ligands

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.1: 5 residues within 4Å: Chain A: N.276, K.278, N.287 Chain C: D.1, Q.27 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.1, C:D.1 NAG-NAG.3: 4 residues within 4Å: Chain B: E.147, E.150, N.154, T.156 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.147 NAG-NAG.7: 5 residues within 4Å: Chain E: N.276, K.278, N.287 Chain G: D.1, Q.27 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:D.1, G:D.1 NAG-NAG.9: 4 residues within 4Å: Chain F: E.147, E.150, N.154, T.156 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:E.147 NAG-NAG.13: 5 residues within 4Å: Chain I: N.276, K.278, N.287 Chain K: D.1, Q.27 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:D.1, K:D.1 NAG-NAG.15: 4 residues within 4Å: Chain J: E.147, E.150, N.154, T.156 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:E.147

3 x NAG- NAG- BMA- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-FUC.2: 3 residues within 4Å: Chain A: N.166, N.237 Chain I: S.218 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.8: 3 residues within 4Å: Chain A: S.218 Chain E: N.166, N.237 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.14: 3 residues within 4Å: Chain E: S.218 Chain I: N.166, N.237 No protein-ligand interaction detected (PLIP)

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

NAG.4: 3 residues within 4Å: Chain A: Q.16, N.24 Chain H: T.74 3 PLIP interactions: 2 interactions with chain H, 1 interactions with chain A Hydrogen bonds: H:T.74, H:T.74, A:Q.16 NAG.5: 1 residues within 4Å: Chain A: N.12 No protein-ligand interaction detected (PLIP) NAG.6: 1 residues within 4Å: Chain A: N.155 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.155 NAG.10: 3 residues within 4Å: Chain E: Q.16, N.24 Chain L: T.74 3 PLIP interactions: 2 interactions with chain L, 1 interactions with chain E Hydrogen bonds: L:T.74, L:T.74, E:Q.16 NAG.11: 1 residues within 4Å: Chain E: N.12 No protein-ligand interaction detected (PLIP) NAG.12: 1 residues within 4Å: Chain E: N.155 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.155 NAG.16: 3 residues within 4Å: Chain D: T.74 Chain I: Q.16, N.24 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain I Hydrogen bonds: D:T.74, D:T.74, I:Q.16 NAG.17: 1 residues within 4Å: Chain I: N.12 No protein-ligand interaction detected (PLIP) NAG.18: 1 residues within 4Å: Chain I: N.155 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:N.155

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, N.C. et al., The D3-9 gene segment encodes for recurring and adaptable binding motifs in broadly neutralizing antibodies to influenza virus. Cell Host Microbe (2018)

Release Date

2018-09-26

Peptides

Hemagglutinin HA1: AEI
Hemagglutinin HA2: BFJ
antibody S9-3-37 light chain: CGK
antibody S9-3-37 heavy chain: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
A

I
A

B
B

F
B

J
B

C
L

G
L

K
L

D
H

H
H

L
H

Hemagglutinin HA1

Hemagglutinin HA2

antibody S9-3-37 light chain

antibody S9-3-37 heavy chain