SMTL ID : 8zy3.1

Sarbecovirus BANAL-20-236 Spike Trimer in a Locked Conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

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: 3 residues within 4Å: Chain A: N.793, S.795, Q.796 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: T.108, N.233, T.235 Chain C: N.456 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain B: N.793, S.795, Q.796, F.809 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.456 Chain B: T.108, N.233, T.235 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain C: N.793, S.795, Q.796, F.809 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 7 residues within 4Å: Chain B: R.453, N.456, K.458, E.461 Chain C: T.108, N.233, T.235 No protein-ligand interaction detected (PLIP)

48 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.7: 1 residues within 4Å: Chain A: N.18 Ligand excluded by PLIP NAG.8: 4 residues within 4Å: Chain A: T.30, N.31, Y.60, N.214 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: F.29, N.62 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: N.164 Chain C: T.466 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain A: N.122, T.124, N.125, I.127 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: E.277, N.278 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: N.327, Q.576 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain A: N.339 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: N.366 Chain C: Y.485 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.612, T.614 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.653 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.701 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain A: N.709, L.914, Q.918, Q.1063 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: E.1064, N.1066 Chain B: Q.887 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain A: N.1090, T.1092, H.1093, F.1095 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.1126 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: C.16, N.18, Y.137 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain B: T.30, N.31, Y.60, N.214 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: F.29, N.62 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: A.163, N.164 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain B: N.122, T.124, N.125, I.127 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: E.277, N.278 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: N.327, Q.576, L.578 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.339 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain A: F.452, Y.485 Chain B: N.366 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: N.612, T.614 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain B: N.653 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain B: N.701 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain B: N.709, L.914, Q.918, Q.1063 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain B: A.698, E.1064, N.1066 Chain C: Q.887 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain B: N.1090, T.1092, H.1093, F.1095 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain B: N.1126 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain C: N.18 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: N.31, Y.60, N.214 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: F.29, N.62 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain C: N.164 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: N.122, N.125 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: E.277, N.278 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: N.327, Q.576 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain C: N.339, S.367, T.368, L.437 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain B: F.452, Y.485 Chain C: N.366 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain C: N.612, T.614 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain C: N.653 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain C: N.701 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain C: N.709, Q.918, Q.1063 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain A: Q.887 Chain C: A.698, E.1064, N.1066 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain C: N.1090, T.1092, H.1093, F.1095 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain C: N.1126 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, J. et al., A locked conformation of spike protein trimer of Sarbecovirus. To Be Published

Release Date

2025-02-05

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein