SMTL ID : 7qdh.1

SARS-CoV-2 S protein S:D614G mutant 1-up

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 4.20 Å

Oligo State

homo-trimer

Ligands

10 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG-NAG.1: 2 residues within 4Å: Chain A: N.700, L.905 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain B: N.700, L.905, Q.909 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain C: N.700, L.905, Q.909 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: F.324, G.325, N.329, S.357 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: N.150, N.151 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: N.317, Q.566, T.567, L.568 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain B: G.1068, N.1117 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain B: N.329 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain C: N.268 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain C: G.325, E.326, N.329 No protein-ligand interaction detected (PLIP)

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

NAG.11: 3 residues within 4Å: Chain A: T.94, N.220, T.222 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain A: N.1117 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: N.692 Chain B: D.779 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: N.784, S.786 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: Y.14, N.47 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: A.689, N.1057 Chain B: Q.878 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: N.1081, T.1083, F.1086 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.268 Chain C: K.544 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.602 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: T.94, N.220 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain B: N.602, T.604, E.605 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain B: N.692, I.1113, G.1114 Chain C: D.779 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: N.1081, H.1084, F.1086 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: N.150, N.151 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.268 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: H.641, N.643 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: N.784, S.786 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: E.1055, N.1057 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain C: N.1117 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: N.1081, T.1083, H.1084 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: A.689, E.1055, N.1057 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain A: D.779 Chain C: N.692, I.1113 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: N.784, S.786 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: N.602, T.604 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ginex, T. et al., The structural role of SARS-CoV-2 genetic background in the emergence and success of spike mutations: The case of the spike A222V mutation. Plos Pathog. (2022)

Release Date

2022-05-25

Peptides

Spike glycoprotein,Fibritin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein,Fibritin