SMTL ID : 8sj9.1

Crystal structure of the H1 hemagglutinin COBRA X6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.25 Å

Oligo State

homo-trimer

Ligands

3 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: 8 residues within 4Å: Chain A: N.69, E.71, E.91, N.92, C.95, S.139, S.141, R.225 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 2 residues within 4Å: Chain C: N.28, T.30 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 6 residues within 4Å: Chain C: N.69, E.71, E.91, N.92, C.95, R.225 No protein-ligand interaction detected (PLIP)

2 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: 7 residues within 4Å: Chain B: N.59, N.69, E.71, E.91, N.92, R.225 Ligands: NAG.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.59 NAG-NAG.5: 6 residues within 4Å: Chain C: V.35, E.39, N.291, S.293, L.294, I.387 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.35

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

NAG.6: 1 residues within 4Å: Chain A: N.16 No protein-ligand interaction detected (PLIP) NAG.7: 3 residues within 4Å: Chain A: N.164, Y.202, N.249 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.202, A:N.249 NAG.8: 2 residues within 4Å: Chain A: T.20, N.28 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.28 NAG.11: 3 residues within 4Å: Chain B: N.59 Ligands: NAG-NAG.2, NAG-NAG.2 No protein-ligand interaction detected (PLIP) NAG.12: 3 residues within 4Å: Chain B: T.20, N.28, K.315 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.20 NAG.13: 2 residues within 4Å: Chain B: N.164, Y.202 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.164, B:Y.202 NAG.14: 5 residues within 4Å: Chain B: S.127, P.129, N.130, P.163, N.164 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.164 NAG.16: 2 residues within 4Å: Chain C: N.59, E.91 No protein-ligand interaction detected (PLIP) NAG.17: 2 residues within 4Å: Chain C: N.164, Y.202 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.202 NAG.18: 1 residues within 4Å: Chain C: N.16 No protein-ligand interaction detected (PLIP)

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 4 residues within 4Å: Chain A: L.430 Chain B: N.426, L.433 Chain C: L.433 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nagashima, K.A. et al., Structural basis for the broad antigenicity of the computationally optimized influenza hemagglutinin X6. Structure (2024)

Release Date

2024-05-01

Peptides

Hemagglutinin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Hemagglutinin