SMTL ID : 7v77.1

Cryo-EM structure of SARS-CoV-2 S-Beta variant (B.1.351), uncleavable form, two RBD-up conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

30 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: 4 residues within 4Å: Chain A: Q.115, E.132, N.165 Chain C: L.515 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.115 NAG-NAG.2: 3 residues within 4Å: Chain A: N.277, E.278, N.279 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.328, Q.577, T.578, L.579 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 7 residues within 4Å: Chain A: F.335, F.339, N.340, L.365, S.368, A.369, S.370 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.369, A:S.370 NAG-NAG.5: 2 residues within 4Å: Chain A: N.613, T.615 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: N.706, I.1127, G.1128 Chain B: D.793 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: N.714, Q.923, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain A: S.701, A.703, K.1070, N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain A: N.1095, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 1 residues within 4Å: Chain A: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 5 residues within 4Å: Chain A: L.515 Chain B: Q.115, E.132, N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain B: E.278, N.279 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain B: F.335, G.336, N.340 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain B: N.613, Q.641 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 2 residues within 4Å: Chain B: N.706 Chain C: D.793 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 2 residues within 4Å: Chain B: N.714, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain B: S.701, A.703, N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 1 residues within 4Å: Chain B: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 3 residues within 4Å: Chain B: K.555 Chain C: E.278, N.279 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain C: N.328, P.576, Q.577, L.579 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 2 residues within 4Å: Chain C: N.613, T.615 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 3 residues within 4Å: Chain A: D.793 Chain C: N.706, I.1127 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 1 residues within 4Å: Chain C: N.714 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 1 residues within 4Å: Chain C: N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 1 residues within 4Å: Chain C: N.1131 No protein-ligand interaction detected (PLIP)

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

NAG.31: 3 residues within 4Å: Chain A: Y.28, N.30, N.61 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain A: G.232, I.233, N.234 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain A: N.600, T.601 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain A: H.652, N.654 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain B: Y.28, T.29, N.30, N.61 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain B: N.122, A.123, V.171 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain B: G.232, I.233, N.234 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain B: N.328, Q.577, T.578 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain B: N.600, T.601 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain B: H.652, N.654 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: N.122, T.124, N.125 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: N.164, N.165 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: T.108, N.234, T.236 Ligand excluded by PLIP NAG.45: 6 residues within 4Å: Chain C: F.339, N.340, S.368, S.370, F.371, W.433 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain C: N.600 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain C: N.654 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, T.J. et al., Cryo-EM structure of SARS-CoV-2 S-Beta variant (B.1.351), uncleavable form, two RBD-up conformation. To Be Published

Release Date

2021-10-06

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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