SMTL ID : 6zwv.1

Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: 3 Closed RBDs

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

15 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: T.108, N.234, T.236 Chain B: E.465 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: N.717, L.922, N.925, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.1098, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: T.108, N.234, T.236 Chain C: E.465 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain B: N.717, L.922, N.925, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain B: N.1098, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain A: E.465 Chain C: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 5 residues within 4Å: Chain C: N.717, L.922, N.925, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain C: N.1098, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP)

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

NAG.16: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.122, T.124 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: E.281, N.282 Chain B: K.558 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: N.331, T.333, Q.580 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: G.339, N.343, L.368 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: N.709, G.1131 Chain C: D.796 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: A.706, N.1074 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: E.132, N.165 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: N.122, T.124 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: E.281, N.282 Chain C: K.558 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: N.331, T.333, Q.580 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: G.339, N.343, L.368 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: N.616, T.618 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain A: D.796 Chain B: N.709, G.1131 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: A.706, N.1074 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: E.132, N.165 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: N.122, T.124 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain A: K.558 Chain C: E.281, N.282 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: N.331, T.333, Q.580 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: G.339, N.343, L.368 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: N.616, T.618 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain B: D.796 Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: A.706, N.1074 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain C: E.132, N.165 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ke, Z. et al., Structures and distributions of SARS-CoV-2 spike proteins on intact virions. Nature (2020)

Release Date

2020-08-05

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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