SMTL ID : 7wg9.1

Delta Spike Trimer(1 RBD Up)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

13 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.715, L.920, Q.924 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.799, S.801, Q.802 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.1096, T.1098, H.1099, F.1101 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain A: N.1132 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: N.715, L.920, Q.1069 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain B: N.799, S.801 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain B: N.1096, T.1098, H.1099, F.1101 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain B: I.1130, N.1132 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain B: D.794 Chain C: S.706, N.707, N.708 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain C: N.715, L.920 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain C: N.799, S.801 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 5 residues within 4Å: Chain C: N.1096, T.1098, H.1099, F.1101, Y.1108 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 1 residues within 4Å: Chain C: N.1132 No protein-ligand interaction detected (PLIP)

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

NAG.14: 3 residues within 4Å: Chain A: Y.28, F.59, N.61 Ligand excluded by PLIP NAG.15: 5 residues within 4Å: Chain A: N.122, K.147, N.148, M.153, E.154 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: E.279, N.280 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.329, Q.578 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: G.337, F.340, N.341 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.601 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.614 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.655 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: N.707 Chain C: D.794 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: E.1070, N.1072 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: E.132, N.162, N.163 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: T.108, N.232 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.27: 6 residues within 4Å: Chain B: N.122, Y.144, K.147, M.153, E.154, S.155 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: E.279, N.280 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: N.329, I.330, Q.578 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: G.337, F.340, N.341 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain B: N.614 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: H.653, N.655 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: S.706, N.707 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain B: A.704, E.1070, N.1072 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain B: N.163 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: N.601, T.602 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: N.232, T.234 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: Y.28, N.30, N.61 Ligand excluded by PLIP NAG.39: 5 residues within 4Å: Chain C: N.122, T.124, K.147, E.154, S.155 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: E.279, N.280 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: N.329, P.577, Q.578 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: G.337, N.341 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: N.614, T.616 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: H.653, N.655 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain B: Q.893 Chain C: N.1072 Ligand excluded by PLIP NAG.46: 5 residues within 4Å: Chain C: S.112, E.132, Q.134, N.162, N.163 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: I.231, N.232 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain C: N.601, T.602 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
A

B
B

C
C

Spike glycoprotein