SMTL ID : 8ajl.1

Structure of the Ancestral Scaffold Antigen-6 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.216, T.218 Chain B: R.433, H.434, G.435, K.436, L.437, K.438, E.441 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 8 residues within 4Å: Chain A: T.687, N.688, N.890, Q.893, Q.897, K.900, Q.1042, F.1080 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: D.767, N.772, S.774, Q.775 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.775, A:Q.775 NAG-NAG.4: 11 residues within 4Å: Chain B: S.94, T.95, N.216, T.218 Chain C: R.433, H.434, G.435, K.436, L.437, K.438, E.441 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 9 residues within 4Å: Chain B: T.687, N.688, F.689, N.890, Q.893, Q.897, K.900, Q.1042, F.1080 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: D.767, N.772, S.774, Q.775 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.775, B:Q.775 NAG-NAG.7: 11 residues within 4Å: Chain A: R.433, H.434, G.435, K.436, L.437, K.438, E.441 Chain C: S.94, T.95, N.216, T.218 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 9 residues within 4Å: Chain C: T.687, N.688, F.689, N.890, Q.893, Q.897, K.900, Q.1042, F.1080 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain C: D.767, N.772, S.774, Q.775 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.775

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

NAG.10: 3 residues within 4Å: Chain A: Q.15, N.48, P.606 Ligand excluded by PLIP NAG.11: 7 residues within 4Å: Chain A: N.108, S.109, T.110, H.111, V.113, H.136, V.153 Ligand excluded by PLIP NAG.12: 5 residues within 4Å: Chain A: N.307, P.554, K.555, T.556, L.557 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain A: N.591, C.592, Q.619 Chain C: Q.807 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: H.630, V.631, N.632 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain A: N.680, N.681, I.1101, G.1102 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: A.677, T.682, N.1045 Ligand excluded by PLIP NAG.17: 6 residues within 4Å: Chain A: R.1044, N.1069, G.1070, T.1071, S.1072, F.1074 Ligand excluded by PLIP NAG.18: 5 residues within 4Å: Chain A: R.146, N.147 Chain B: Y.327, A.328, I.444 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain A: D.256, E.257, N.258 Chain B: R.533 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: N.319, S.347, T.348, L.417 Ligand excluded by PLIP NAG.21: 6 residues within 4Å: Chain A: N.12, T.14, L.53, L.55, R.64, R.196 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain A: N.98, Q.120, T.143, R.146 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain A: N.346 Chain B: L.432, Y.464, N.468 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: I.1104, N.1105 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: Q.15, N.48, P.606 Ligand excluded by PLIP NAG.26: 7 residues within 4Å: Chain B: N.108, S.109, T.110, H.111, V.113, H.136, V.153 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: N.307, K.555, L.557 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain A: Q.807 Chain B: N.591, Q.619 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: H.630, V.631, N.632 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain B: N.680, N.681, I.1101, G.1102 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain A: Q.866 Chain B: A.677, E.1043, N.1045 Ligand excluded by PLIP NAG.32: 6 residues within 4Å: Chain B: R.1044, N.1069, G.1070, T.1071, S.1072, F.1074 Ligand excluded by PLIP NAG.33: 5 residues within 4Å: Chain B: R.146, N.147 Chain C: Y.327, A.328, I.444 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain B: D.256, E.257, N.258 Chain C: R.533 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: N.319, S.347, L.417 Ligand excluded by PLIP NAG.36: 5 residues within 4Å: Chain B: N.12, T.14, R.51, L.53, R.64 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain B: N.98, T.99, Q.120, R.146 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain B: N.346 Chain C: L.432, Y.464, N.468 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain B: N.1105 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain C: Q.15, N.48, P.606, R.609 Ligand excluded by PLIP NAG.41: 6 residues within 4Å: Chain C: N.108, S.109, T.110, H.111, V.113, V.153 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: N.307, P.554, K.555 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain B: Q.807 Chain C: N.591, Q.619 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: H.630, N.632 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain C: N.680, N.681, I.1101, G.1102 Ligand excluded by PLIP NAG.46: 5 residues within 4Å: Chain B: Q.866 Chain C: A.677, E.1043, R.1044, N.1045 Ligand excluded by PLIP NAG.47: 6 residues within 4Å: Chain C: R.1044, N.1069, G.1070, T.1071, S.1072, F.1074 Ligand excluded by PLIP NAG.48: 5 residues within 4Å: Chain A: Y.327, A.328, I.444 Chain C: R.146, N.147 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain A: R.533 Chain C: D.256, E.257, N.258 Ligand excluded by PLIP NAG.50: 4 residues within 4Å: Chain C: N.319, S.347, T.348, L.417 Ligand excluded by PLIP NAG.51: 5 residues within 4Å: Chain C: N.12, T.14, R.51, L.53, R.64 Ligand excluded by PLIP NAG.52: 5 residues within 4Å: Chain C: D.97, N.98, T.99, Q.120, R.146 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain A: L.432, Y.464, N.468 Chain C: N.346 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain C: I.1104, N.1105 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
C

C
B

Spike glycoprotein,Fibritin