SMTL ID : 7ub5.1

SARS-CoV-2 Omicron-BA.2 3-RBD down Spike Protein Trimer without the P986-P987 stabilizing mutations (S-GSAS-Omicron-BA.2)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

10 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: 6 residues within 4Å: Chain A: T.105, N.231, T.233 Chain C: R.454, K.455, S.456 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.455, C:S.456, C:S.456 NAG-NAG.2: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: Y.25, N.58 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.714, L.919, Q.923, Q.1068 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.919 NAG-NAG.5: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain C: N.714, L.919, Q.923, Q.1068 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.919 NAG-NAG.10: 2 residues within 4Å: Chain C: N.798, S.800 No protein-ligand interaction detected (PLIP)

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

NAG.11: 3 residues within 4Å: Chain A: E.129, F.130, N.162 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.279 Chain C: K.555 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: N.328, P.576, Q.577 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: N.340, F.368 Ligand excluded by PLIP NAG.15: 5 residues within 4Å: Chain A: N.613, T.615, Q.641 Chain B: I.831, K.832 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.706 Chain B: I.791 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: A.703, E.1069, N.1071 Chain B: Q.892 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.1131 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain A: N.119, A.120, T.121, N.122 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: Y.25, N.58 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain B: N.119, A.120, N.122, V.124 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: A.160, N.161, N.162 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain A: S.456, K.459 Chain B: T.105, N.231 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: K.555 Chain B: N.277, N.279 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.613 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.706 Chain C: Y.793 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: A.703, E.1069, N.1071 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain B: N.1131 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: N.714, Q.923, Q.1068 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain C: Y.25, N.58 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain C: E.278, N.279 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain C: N.328, P.576, Q.577 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: N.340, F.368 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain A: Q.833 Chain C: N.613 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain A: I.791, Y.793 Chain C: N.706 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain C: A.703, E.1069, N.1071 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.1131 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stalls, V. et al., Cryo-EM structures of SARS-CoV-2 Omicron BA.2 spike. Cell Rep (2022)

Release Date

2022-04-20

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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