SMTL ID : 8fu8.1

Structure of Covid Spike variant deltaN135 with one erect RBD

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: N.315, Q.564 Ligand excluded by PLIP NAG.2: 1 residues within 4Å: Chain A: N.587 Ligand excluded by PLIP NAG.3: 3 residues within 4Å: Chain A: G.323, F.326, N.327 Ligand excluded by PLIP NAG.4: 2 residues within 4Å: Chain A: N.122, N.125 Ligand excluded by PLIP NAG.5: 1 residues within 4Å: Chain A: A.154 Ligand excluded by PLIP NAG.6: 4 residues within 4Å: Chain A: T.108, N.225, T.227 Chain C: E.449 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: E.265, N.266 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain A: N.641 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: N.693, I.1114, G.1115 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: N.701, Q.1055 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: N.785, Q.788, N.912 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: A.690, E.1056, N.1058 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain A: F.59, S.60, N.61, P.615 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain A: N.1118 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: N.1082, T.1084, F.1087 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: N.600, E.603, Q.628 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: E.449 Chain B: N.225, T.227 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: E.265, N.266 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain B: N.587 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: F.326, N.327 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain B: N.122, T.124, N.125 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain B: N.641 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain B: N.693 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: N.701, Q.1055 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: N.785, S.787, Q.788 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: E.1056, N.1058 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: F.59, N.61, P.615 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: N.315, P.563, Q.564 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.1118 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: N.1082, H.1085, Y.1094 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.600, Q.628 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: E.132, N.155, N.156 Ligand excluded by PLIP NAG.33: 5 residues within 4Å: Chain C: F.322, G.323, F.326, N.327, L.352 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.587 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain C: N.122, A.123, T.124, N.125 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: N.225, T.227 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: N.264, E.265, N.266 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain C: N.641 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain C: N.693 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain C: N.701 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: N.785, S.787 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: A.690, N.1058 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: N.315, I.316, Q.564 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain C: C.1066, I.1116, N.1118 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain C: N.1082, T.1084, F.1087 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: N.600, T.602 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain C: E.132, N.155, N.156 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

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