SMTL ID : 7lwn.1

Mink Cluster 5-associated SARS-CoV-2 spike protein (S-GSAS-D614G-delFV) in the 1-RBD up conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

5 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: 1 residues within 4Å: Chain A: N.1132 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.1096, T.1098, H.1099, F.1101 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 1 residues within 4Å: Chain B: N.1132 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain B: N.1096, T.1098, H.1099, F.1101 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain C: N.1096, T.1098, H.1099, F.1101 No protein-ligand interaction detected (PLIP)

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

NAG.6: 3 residues within 4Å: Chain A: A.704, E.1070, N.1072 Ligand excluded by PLIP NAG.7: 3 residues within 4Å: Chain A: N.799, S.801, Q.802 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain A: N.715, Q.924, Q.1069 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: N.707, G.1129 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: H.653, N.655 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: N.614, T.616 Ligand excluded by PLIP NAG.12: 5 residues within 4Å: Chain A: Q.113, E.130, N.163, T.165 Chain C: I.466 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain B: A.704, E.1070, N.1072 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain B: N.799, S.801, Q.802 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain B: N.715, Q.924, Q.1069 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain B: N.707, G.1129 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: N.614, T.616 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain B: N.655 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: N.329, Q.578 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: N.278, N.280 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: N.162, N.163 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain C: A.704, E.1070, N.1072 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain C: N.799, S.801, Q.802 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain C: N.715, Q.924, Q.1069 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain C: N.707, G.1129 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain C: N.655 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain C: N.614 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain C: N.341 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain C: N.278, N.280 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain C: N.1132 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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