SMTL ID : 6ntf.1

Crystal structure of a computationally optimized H5 influenza hemagglutinin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-trimer

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: E.477, E.480, S.481, N.484, T.486 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.165, N.166, T.167, N.236 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 5 residues within 4Å: Chain B: E.477, E.480, S.481, N.484, T.486 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain B: N.165, N.166, T.167, N.236 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 5 residues within 4Å: Chain C: E.477, E.480, S.481, N.484, T.486 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 4 residues within 4Å: Chain C: N.165, N.166, T.167, N.236 No protein-ligand interaction detected (PLIP)

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

NAG.3: 2 residues within 4Å: Chain A: Q.15, N.23 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.15 NAG.4: 1 residues within 4Å: Chain A: N.154 No protein-ligand interaction detected (PLIP) NAG.5: 1 residues within 4Å: Chain A: N.286 No protein-ligand interaction detected (PLIP) NAG.16: 2 residues within 4Å: Chain B: Q.15, N.23 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.15 NAG.17: 1 residues within 4Å: Chain B: N.154 No protein-ligand interaction detected (PLIP) NAG.18: 1 residues within 4Å: Chain B: N.286 No protein-ligand interaction detected (PLIP) NAG.29: 2 residues within 4Å: Chain C: Q.15, N.23 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.15 NAG.30: 1 residues within 4Å: Chain C: N.154 No protein-ligand interaction detected (PLIP) NAG.31: 1 residues within 4Å: Chain C: N.286 No protein-ligand interaction detected (PLIP)

12 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 9 residues within 4Å: Chain A: V.16, D.17, R.310, L.311, V.312, E.427, V.430, L.431, N.434 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.17, A:D.17, A:V.312, A:E.427, A:E.427, A:N.434 PEG.7: 6 residues within 4Å: Chain A: C.4, W.344, H.355, Y.364, N.465, C.467 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.355, A:Y.364 PEG.8: 4 residues within 4Å: Chain A: D.88, N.94, F.95, Y.98 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.94, A:F.95 Hydrogen bonds: A:D.88 PEG.9: 4 residues within 4Å: Chain A: H.28, V.348, G.350, W.351 No protein-ligand interaction detected (PLIP) PEG.19: 9 residues within 4Å: Chain B: V.16, D.17, R.310, L.311, V.312, E.427, V.430, L.431, N.434 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.17, B:D.17, B:V.312, B:E.427, B:E.427, B:N.434 PEG.20: 6 residues within 4Å: Chain B: C.4, W.344, H.355, Y.364, N.465, C.467 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.355, B:Y.364 PEG.21: 4 residues within 4Å: Chain B: D.88, N.94, F.95, Y.98 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:N.94, B:F.95 Hydrogen bonds: B:D.88 PEG.22: 4 residues within 4Å: Chain B: H.28, V.348, G.350, W.351 No protein-ligand interaction detected (PLIP) PEG.32: 9 residues within 4Å: Chain C: V.16, D.17, R.310, L.311, V.312, E.427, V.430, L.431, N.434 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:D.17, C:D.17, C:V.312, C:E.427, C:E.427, C:N.434 PEG.33: 6 residues within 4Å: Chain C: C.4, W.344, H.355, Y.364, N.465, C.467 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.355, C:Y.364 PEG.34: 4 residues within 4Å: Chain C: D.88, N.94, F.95, Y.98 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:N.94, C:F.95 Hydrogen bonds: C:D.88 PEG.35: 4 residues within 4Å: Chain C: H.28, V.348, G.350, W.351 No protein-ligand interaction detected (PLIP)

12 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 7 residues within 4Å: Chain A: Y.7, H.8, A.9, L.317, R.318, N.319, S.320 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.8, A:R.318, A:S.320 MG.11: 6 residues within 4Å: Chain A: G.6, Y.7, I.340, G.342, G.343, W.344 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:G.342 MG.12: 6 residues within 4Å: Chain A: Y.449, L.463, G.464, N.465, G.466, C.467 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:Y.449, A:C.467 MG.13: 6 residues within 4Å: Chain A: L.52, R.53, C.55, E.81, K.82, P.85 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:L.52, A:R.53, A:C.55 MG.23: 7 residues within 4Å: Chain B: Y.7, H.8, A.9, L.317, R.318, N.319, S.320 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.8, B:R.318, B:S.320 MG.24: 6 residues within 4Å: Chain B: G.6, Y.7, I.340, G.342, G.343, W.344 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:G.342 MG.25: 6 residues within 4Å: Chain B: Y.449, L.463, G.464, N.465, G.466, C.467 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:Y.449, B:C.467 MG.26: 6 residues within 4Å: Chain B: L.52, R.53, C.55, E.81, K.82, P.85 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:L.52, B:R.53, B:C.55 MG.36: 7 residues within 4Å: Chain C: Y.7, H.8, A.9, L.317, R.318, N.319, S.320 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.8, C:R.318, C:S.320 MG.37: 6 residues within 4Å: Chain C: G.6, Y.7, I.340, G.342, G.343, W.344 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:G.342 MG.38: 6 residues within 4Å: Chain C: Y.449, L.463, G.464, N.465, G.466, C.467 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:Y.449, C:C.467 MG.39: 6 residues within 4Å: Chain C: L.52, R.53, C.55, E.81, K.82, P.85 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:L.52, C:R.53, C:C.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bar-Peled, Y. et al., Structural and antigenic characterization of a computationally-optimized H5 hemagglutinin influenza vaccine. Vaccine (2019)

Release Date

2019-09-18

Peptides

Hemagglutinin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Hemagglutinin