SMTL ID : 7r13.1

Alpha Variant SARS-CoV-2 Spike in Closed conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

9 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.745 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.1126, T.1128, H.1129, F.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 1 residues within 4Å: Chain A: N.1162 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain B: N.745 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain B: N.1126, T.1128, H.1129, F.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain B: N.1162 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain C: N.745 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain C: N.1126, T.1128, H.1129, F.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain C: N.1162 No protein-ligand interaction detected (PLIP)

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

NAG.10: 6 residues within 4Å: Chain A: N.151, A.152, T.153, N.154, V.156, K.158 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: N.192, N.193 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: T.137, N.262 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: N.359, P.607, Q.608 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: F.366, G.367, F.370, N.371 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: N.644, T.646, Q.672 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.685 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.737 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: N.829, S.831, Q.832 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: A.734, N.1102 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: Y.59, N.61, N.92 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.310 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.631 Ligand excluded by PLIP NAG.23: 6 residues within 4Å: Chain B: N.151, A.152, T.153, N.154, V.156, K.158 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: N.192, N.193 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: T.137, N.262 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: N.359, P.607, Q.608 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain B: F.366, G.367, F.370, N.371 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: N.644, T.646, Q.672 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.685 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.737 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: N.829, S.831, Q.832 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: A.734, N.1102 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain B: Y.59, N.61, N.92 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain B: N.310 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain B: N.631 Ligand excluded by PLIP NAG.36: 6 residues within 4Å: Chain C: N.151, A.152, T.153, N.154, V.156, K.158 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: N.192, N.193 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: T.137, N.262 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: N.359, P.607, Q.608 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain C: F.366, G.367, F.370, N.371 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: N.644, T.646, Q.672 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain C: N.685 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain A: D.824 Chain C: N.737 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: N.829, S.831, Q.832 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: A.734, N.1102 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain C: Y.59, N.61, N.92 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain C: N.310 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain C: N.631 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wrobel, A.G. et al., Evolution of the SARS-CoV-2 spike protein in the human host. Nat Commun (2022)

Release Date

2022-03-09

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

Related Entries With Identical Sequence