SMTL ID : 7lwm.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

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

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

NAG.4: 1 residues within 4Å: Chain A: N.1132 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain A: A.704, E.1070, N.1072 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain A: N.799, S.801, Q.802 Ligand excluded by PLIP NAG.7: 4 residues within 4Å: Chain A: N.715, L.920, Q.924, Q.1069 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain A: N.707, I.1128, G.1129 Ligand excluded by PLIP NAG.9: 1 residues within 4Å: Chain A: N.655 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: N.614, T.616 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain A: F.340, N.341, S.371, W.434 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain A: N.280 Ligand excluded by PLIP NAG.13: 8 residues within 4Å: Chain A: T.106, N.232, T.234 Chain C: R.455, S.457, N.458, K.460, E.463 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain B: N.1132 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain B: A.704, E.1070, N.1072 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain B: N.799, S.801, Q.802 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain B: N.715, Q.924, Q.1069 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain B: N.707, I.1128, G.1129 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: H.653, V.654, N.655 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain B: N.614, T.616, Q.642 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: N.329, Q.578 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: T.106, N.232, T.234 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: Y.28, N.30, N.61 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain C: N.1132 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain C: E.1070, N.1072 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain C: N.799, S.801, Q.802 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain C: N.715, L.920, Q.924, Q.1069 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain C: N.707, I.1128, G.1129 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain C: N.655 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: N.614, T.616, E.617 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain C: G.337, F.340, N.341, L.366 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: K.556 Chain C: N.280 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: Y.28, N.61 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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