SMTL ID : 8aja.1

Structure of the Ancestral Scaffold Antigen-5 of Coronavirus Spike protein

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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.1: 11 residues within 4Å: Chain A: S.94, T.95, N.214, T.216 Chain C: R.426, K.427, T.428, K.429, L.430, K.431, E.434 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 7 residues within 4Å: Chain A: T.668, N.669, N.871, Q.874, Q.878, Q.1023, F.1061 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: D.748, N.753, S.755, Q.756 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.756 NAG-NAG.4: 11 residues within 4Å: Chain A: R.426, K.427, T.428, K.429, L.430, K.431, E.434 Chain B: S.94, T.95, N.214, T.216 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 8 residues within 4Å: Chain B: N.669, F.670, N.871, Q.874, Q.878, K.881, Q.1023, F.1061 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain B: D.748, N.753, S.755, Q.756, F.769, Q.887 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.756, B:Q.756 NAG-NAG.7: 11 residues within 4Å: Chain B: R.426, K.427, T.428, K.429, L.430, K.431, E.434 Chain C: S.94, T.95, N.214, T.216 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.427 NAG-NAG.8: 8 residues within 4Å: Chain C: T.668, N.669, N.871, Q.874, Q.878, K.881, Q.1023, F.1061 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 6 residues within 4Å: Chain C: D.748, N.753, S.755, Q.756, F.769, Q.887 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.756

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

NAG.10: 2 residues within 4Å: Chain A: I.1085, N.1086 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: Q.15, N.48, P.587 Ligand excluded by PLIP NAG.12: 7 residues within 4Å: Chain A: N.108, S.109, T.110, H.111, I.113, H.134, V.151 Ligand excluded by PLIP NAG.13: 5 residues within 4Å: Chain A: N.305, P.535, Q.536, T.537, L.538 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.572, Q.600 Chain B: Q.788 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: H.611, V.612, N.613 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain A: N.661, N.662, I.1082, G.1083 Ligand excluded by PLIP NAG.17: 5 residues within 4Å: Chain A: A.658, E.1024, R.1025, N.1026 Chain B: Q.847 Ligand excluded by PLIP NAG.18: 6 residues within 4Å: Chain A: R.1025, N.1050, G.1051, T.1052, S.1053, F.1055 Ligand excluded by PLIP NAG.19: 6 residues within 4Å: Chain A: R.144, N.145 Chain C: Y.325, A.326, L.437, N.439 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: N.254, E.255, N.256 Chain C: R.514 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain A: N.317, S.345, T.346, Q.415 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: V.341, N.344 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: I.1085, N.1086 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain B: Q.15, N.48, P.587, R.590 Ligand excluded by PLIP NAG.25: 8 residues within 4Å: Chain B: N.108, S.109, T.110, H.111, I.113, H.134, T.137, V.151 Ligand excluded by PLIP NAG.26: 5 residues within 4Å: Chain B: N.305, P.535, Q.536, T.537, L.538 Ligand excluded by PLIP NAG.27: 5 residues within 4Å: Chain B: N.572, D.575 Chain C: Q.788, Y.789, G.790 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: H.611, V.612, N.613 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: N.661, I.1082, G.1083 Ligand excluded by PLIP NAG.30: 5 residues within 4Å: Chain B: A.658, E.1024, R.1025, N.1026 Chain C: Q.847 Ligand excluded by PLIP NAG.31: 5 residues within 4Å: Chain B: N.1050, G.1051, T.1052, S.1053, F.1055 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain A: Y.325, A.326, L.437 Chain B: N.145 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain A: R.514 Chain B: N.254, E.255, N.256 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain B: N.317, S.345, T.346 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain B: V.341, N.344 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: I.1085, N.1086 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: Q.15, N.48, P.587 Ligand excluded by PLIP NAG.38: 7 residues within 4Å: Chain C: N.108, S.109, T.110, H.111, I.113, H.134, V.151 Ligand excluded by PLIP NAG.39: 5 residues within 4Å: Chain C: N.305, P.535, Q.536, T.537, L.538 Ligand excluded by PLIP NAG.40: 5 residues within 4Å: Chain A: Q.788, Y.789, G.790 Chain C: N.572, D.575 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: H.611, V.612, N.613 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: N.661, I.1082, G.1083 Ligand excluded by PLIP NAG.43: 5 residues within 4Å: Chain A: Q.847 Chain C: A.658, E.1024, R.1025, N.1026 Ligand excluded by PLIP NAG.44: 5 residues within 4Å: Chain C: N.1050, G.1051, T.1052, S.1053, F.1055 Ligand excluded by PLIP NAG.45: 5 residues within 4Å: Chain B: Y.325, A.326, L.437, N.439 Chain C: N.145 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain B: R.514 Chain C: N.254, E.255, N.256 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain C: N.317, S.345, T.346, Q.415 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain C: V.341, N.344 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hueting, D. et al., Design, structure and plasma binding of ancestral beta-CoV scaffold antigens. Nat Commun (2023)

Release Date

2023-08-16

Peptides

Spike glycoprotein,Fibritin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein,Fibritin