SMTL ID : 8fu9.1

Structure of Covid Spike variant deltaN25 with one erect RBD

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: V.107, N.109, K.116, E.143, V.146 Ligand excluded by PLIP NAG.2: 2 residues within 4Å: Chain A: N.262 Chain C: K.538 Ligand excluded by PLIP NAG.3: 2 residues within 4Å: Chain A: N.689, G.1111 Ligand excluded by PLIP NAG.4: 5 residues within 4Å: Chain A: N.697, F.698, L.902, Q.906, Q.1051 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain A: N.781, S.783, Q.784 Ligand excluded by PLIP NAG.6: 2 residues within 4Å: Chain A: A.686, N.1054 Ligand excluded by PLIP NAG.7: 4 residues within 4Å: Chain A: N.1078, T.1080, H.1081, F.1083 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain A: N.1114 Ligand excluded by PLIP NAG.9: 1 residues within 4Å: Chain A: N.637 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain A: N.583 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain A: Y.28, T.29, N.30, N.61 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.596, Q.624 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: N.311, Q.560, T.561 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain B: Y.28, T.29, N.30, N.61 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain B: E.261, N.262 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain B: N.596, C.597, Q.624 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: N.689, G.1111 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain B: A.686, E.1052, K.1053, N.1054 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: N.697, Q.1051 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain B: N.1078, T.1080, H.1081, F.1083 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain B: N.1114 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain B: N.637 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: N.781, S.783 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain B: N.583 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: N.311, Q.560 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain C: N.260, E.261, N.262 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain C: N.596, T.598 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain A: D.776 Chain C: N.689 Ligand excluded by PLIP NAG.30: 5 residues within 4Å: Chain C: N.697, F.698, L.902, Q.906, Q.1051 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain C: N.781, S.783 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain C: N.1054 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain C: N.1114 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: F.318, G.319, N.323 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain C: N.637 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain C: N.1078, H.1081, F.1083 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: N.583, T.584 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: N.311, Q.560 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, X. et al., Convergence of immune escape strategies highlights plasticity of SARS-CoV-2 spike. Plos Pathog. (2023)

Release Date

2023-04-05

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein