SMTL ID : 7ybh.1

SARS-CoV-2 lambda variant spike

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.50 Å

Oligo State

homo-trimer

Ligands

15 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: G.332, N.336 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.702 Chain C: D.789 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain A: S.704, N.1067 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain B: N.324, Q.573, T.574 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain A: D.789 Chain B: N.702 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain B: N.275 Chain C: K.551 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain B: N.609, Q.637 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 2 residues within 4Å: Chain B: N.794, S.796 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 2 residues within 4Å: Chain B: S.704, N.1067 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 1 residues within 4Å: Chain B: N.1127 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 1 residues within 4Å: Chain C: N.275 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 2 residues within 4Å: Chain C: G.332, N.336 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 2 residues within 4Å: Chain C: N.702, G.1124 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 2 residues within 4Å: Chain C: N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 2 residues within 4Å: Chain C: A.699, N.1067 No protein-ligand interaction detected (PLIP)

15 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.3: 2 residues within 4Å: Chain A: N.324, Q.573 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 2 residues within 4Å: Chain A: N.710, L.915 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 3 residues within 4Å: Chain A: N.794, S.796, Q.797 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 2 residues within 4Å: Chain A: I.1125, N.1127 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 2 residues within 4Å: Chain B: N.122, T.124 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 2 residues within 4Å: Chain B: N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 7 residues within 4Å: Chain B: T.108, N.234, T.236 Chain C: R.450, S.452, N.453, K.455 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.16: 2 residues within 4Å: Chain B: N.710, Q.1064 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 4 residues within 4Å: Chain B: N.1091, T.1093, H.1094, F.1096 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.24: 2 residues within 4Å: Chain C: N.122, E.154 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.26: 2 residues within 4Å: Chain C: N.609, T.611 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.27: 3 residues within 4Å: Chain C: N.710, Q.919, Q.1064 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.28: 3 residues within 4Å: Chain C: N.794, S.796, Q.797 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.30: 3 residues within 4Å: Chain C: N.1091, T.1093, H.1094 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.31: 1 residues within 4Å: Chain C: N.1127 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.7: 3 residues within 4Å: Chain A: N.1091, T.1093, H.1094 No protein-ligand interaction detected (PLIP)

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

NAG.32: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain A: N.122, T.124 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain A: N.165 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain A: T.108, N.234 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain A: N.275 Chain B: K.551 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain A: N.596 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain A: N.650 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain A: N.609 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain B: Y.28, F.59, N.61, P.624 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain B: N.336 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain B: N.596 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain B: H.648, V.649, N.650 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: N.234, T.236 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain C: N.324 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: E.302, N.596 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain C: N.650 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xing, X. et al., Structures of SARS-CoV-2 spike protein alert noteworthy sites for the potential approaching variants. Virol Sin (2022)

Release Date

2023-08-09

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein