SMTL ID : 7qdg.1

SARS-CoV-2 S protein S:A222V + S:D614G mutant 1-up

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.40 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)

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 A: N.329, S.357, A.358 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: N.150, N.151 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain B: N.700, Q.909 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain B: N.317, L.568 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain B: G.1068, N.1117 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.329, N.356, S.357 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.357 NAG-NAG.8: 2 residues within 4Å: Chain B: N.784, S.786 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain C: N.700, Q.909 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain C: E.267, N.268 No protein-ligand interaction detected (PLIP)

1 x NDG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose(Non-covalent)

NDG-NAG.11: 1 residues within 4Å: Chain C: N.329 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.329

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

NAG.12: 3 residues within 4Å: Chain A: T.94, N.220, T.222 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain A: N.1117 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain A: N.692 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: N.784, S.786 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: Y.14, N.47 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.317, Q.566 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: A.689, N.1057 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: N.1081, T.1083, F.1086 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.268 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: N.602, T.604 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: T.94, N.220 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: N.602, T.604, Q.630 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: N.692, I.1113 Chain C: D.779 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: N.1081, H.1084, F.1086 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.150, N.151 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain A: K.544 Chain B: N.266, N.268 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: H.641, N.643 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.1057 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: C.1065, C.1109, N.1117 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain C: N.1081, T.1083, H.1084, F.1086 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain C: A.689, E.1055, N.1057 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain A: D.779 Chain C: N.692, G.1114 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: N.784, S.786 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain C: N.602 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain C: N.317, P.565, Q.566 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