SMTL ID : 7q1z.1

Structure of formaldehyde cross-linked SARS-CoV-2 S glycoprotein

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(Non-covalent)(Post Translational Modification)

NAG-NAG.1: 1 residues within 4Å: Chain A: N.234 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.1098, T.1100, 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: 1 residues within 4Å: Chain B: N.234 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain B: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain B: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain B: N.1098, T.1100, 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: 2 residues within 4Å: Chain C: N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain C: N.717, L.922, 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: 4 residues within 4Å: Chain C: N.1098, T.1100, 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)(Non-covalent)

NAG.16: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: N.122, N.125, V.127, K.129 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.282 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain A: P.330, N.331, P.579, Q.580 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: F.338, 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, Q.644 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: N.709, G.1131 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain A: N.165 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.61 Ligand excluded by PLIP NAG.28: 5 residues within 4Å: Chain B: N.122, N.125, V.127, K.129, E.169 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.282 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain B: P.330, N.331, P.579, Q.580 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: F.338, 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, Q.644 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: H.655, N.657 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain B: N.709, G.1131 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain B: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain B: N.165 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain C: N.122, N.125, V.127, K.129 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain C: N.282 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain C: P.330, N.331, P.579, Q.580 Ligand excluded by PLIP NAG.42: 5 residues within 4Å: Chain C: F.338, G.339, F.342, 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, Q.644 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: H.655, N.657 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain C: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain C: N.165 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sulbaran, G. et al., Immunization with synthetic SARS-CoV-2 S glycoprotein virus-like particles protects macaques from infection. Cell Rep Med (2022)

Release Date

2022-03-09

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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