SMTL ID : 7wg8.1

Delta Spike Trimer(3 RBD Down)

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: 2 residues within 4Å: Chain A: N.702, L.907 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.786, S.788, Q.789 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 1 residues within 4Å: Chain B: N.702 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: N.786, S.788, Q.789 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain C: N.702, Q.911, Q.1056 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain C: N.786, S.788 No protein-ligand interaction detected (PLIP)

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

NAG.7: 2 residues within 4Å: Chain A: Y.15, N.48 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain A: N.109, A.110, T.111 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: T.95, N.219 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: E.266, N.267 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: N.316, Q.565 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: F.327, N.328 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain A: N.588 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: N.601, T.603 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.642 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.694 Chain C: D.781 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: A.691, N.1059 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain A: N.1083, T.1085, H.1086, F.1088 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.1119 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: Y.15, N.48 Ligand excluded by PLIP NAG.21: 6 residues within 4Å: Chain B: V.107, N.108, N.109, T.111, N.112, V.114 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: T.95, N.219 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: E.266, N.267 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: N.316, Q.565 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.328 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.588 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: N.601, T.603, Q.629 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain B: N.642 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.694 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: A.691, N.1059 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain B: N.1083, T.1085, H.1086, F.1088 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.1119 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: Y.15, N.48 Ligand excluded by PLIP NAG.34: 5 residues within 4Å: Chain C: N.109, A.110, T.111, N.112, V.114 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: T.95, N.219 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: E.266, N.267 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.316 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: F.327, N.328, L.353 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: N.588, T.589 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: N.601, T.603 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain C: N.642 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain B: D.781 Chain C: N.694, G.1116 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain C: N.1059 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain C: N.1083, T.1085, H.1086, F.1088 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain C: N.1119 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cui, Z. et al., Structural and functional characterizations of infectivity and immune evasion of SARS-CoV-2 Omicron. Cell (2022)

Release Date

2022-06-22

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
C

Spike glycoprotein