SMTL ID : 7lwp.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: T.106, N.232, T.234 Ligand excluded by PLIP NAG.2: 1 residues within 4Å: Chain A: N.280 Ligand excluded by PLIP NAG.3: 7 residues within 4Å: Chain A: T.305, V.306, E.307, G.599, T.600, N.601, T.602 Ligand excluded by PLIP NAG.4: 4 residues within 4Å: Chain A: N.614, T.616, Q.642, R.644 Ligand excluded by PLIP NAG.5: 2 residues within 4Å: Chain A: H.653, N.655 Ligand excluded by PLIP NAG.6: 2 residues within 4Å: Chain A: N.707, G.1129 Ligand excluded by PLIP NAG.7: 3 residues within 4Å: Chain A: N.715, Q.924, Q.1069 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain A: A.704, E.1070, N.1072 Ligand excluded by PLIP NAG.9: 4 residues within 4Å: Chain A: N.1096, T.1098, H.1099, F.1101 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain A: N.1132 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: N.799, S.801, Q.802 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain B: E.279, N.280 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain B: N.329, Q.578 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain B: N.614 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain B: N.655 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain B: N.707, I.1128, G.1129 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: N.715, Q.924 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain B: N.799, S.801, Q.802 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: A.704, N.1072 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain B: N.1096, T.1098, H.1099, F.1101 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain B: N.1132 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain C: S.46, E.279, N.280 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain C: N.329, Q.578 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain C: N.614, T.616 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain C: N.655 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain A: D.794 Chain C: N.707, G.1129 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain C: N.715, Q.924, Q.1069 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain C: N.799, S.801 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain C: A.704, E.1070, K.1071, N.1072 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain C: N.1096, T.1098, H.1099, F.1101 Ligand excluded by PLIP NAG.31: 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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