SMTL ID : 7lwq.1

Mink Cluster 5-associated SARS-CoV-2 spike protein(S-GSAS-D614G-delFV) missing the S1 subunit and SD2 subdomain of one protomer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

1 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: 2 residues within 4Å: Chain B: I.1130, N.1132 No protein-ligand interaction detected (PLIP)

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

NAG.2: 3 residues within 4Å: Chain A: Y.28, F.59, N.61 Ligand excluded by PLIP NAG.3: 5 residues within 4Å: Chain A: N.120, N.123, V.124, V.169, S.170 Ligand excluded by PLIP NAG.4: 2 residues within 4Å: Chain A: N.278, N.280 Ligand excluded by PLIP NAG.5: 6 residues within 4Å: Chain A: N.329, I.330, T.331, K.527, S.528, N.530 Ligand excluded by PLIP NAG.6: 2 residues within 4Å: Chain A: N.601, T.602 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: N.614, T.616 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain A: N.655 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: N.707, G.1129 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain A: A.704, E.1070, N.1072 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain A: E.130, N.163, T.165 Chain C: I.466 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain A: N.1132 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain A: N.1096, T.1098, H.1099, F.1101 Ligand excluded by PLIP NAG.14: 5 residues within 4Å: Chain B: N.707, I.1128, G.1129 Chain C: I.792, D.794 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain B: A.704, N.1072 Ligand excluded by PLIP NAG.16: 5 residues within 4Å: Chain B: N.1096, T.1098, H.1099, F.1101, Y.1108 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain C: Y.28, T.29, N.61 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain C: N.278, E.279, N.280 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain C: N.329 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain C: N.601, T.602 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain C: E.1070, N.1072 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain C: N.614, T.616 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain C: K.111, T.112, E.130, N.163 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain C: H.653, N.655 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain C: N.707, I.1128 Ligand excluded by PLIP NAG.26: 5 residues within 4Å: Chain C: V.118, N.120, T.122, V.125, L.139 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain C: N.1132 Ligand excluded by PLIP NAG.28: 6 residues within 4Å: Chain C: S.1095, N.1096, T.1098, H.1099, F.1101, Y.1108 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gobeil, S.M. et al., Effect of natural mutations of SARS-CoV-2 on spike structure, conformation, and antigenicity. Science (2021)

Release Date

2021-03-31

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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