SMTL ID : 7ybk.1

SARS-CoV-2 B.1.620 variant spike (open state)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.90 Å

Oligo State

homo-trimer

Ligands

19 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: 4 residues within 4Å: Chain A: C.15, V.16, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.324, Q.573 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.609, T.611, Q.637 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.710, L.915, N.918, Q.919 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.918 NAG-NAG.5: 2 residues within 4Å: Chain A: N.794, S.796 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain B: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 6 residues within 4Å: Chain B: N.122, T.124, V.127, K.129, E.154, V.171 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.171 NAG-NAG.11: 3 residues within 4Å: Chain B: E.132, N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain B: E.274, N.275 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 1 residues within 4Å: Chain B: N.609 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain B: N.710, T.712, L.915 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 1 residues within 4Å: Chain B: N.794 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 4 residues within 4Å: Chain C: C.15, V.16, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 3 residues within 4Å: Chain C: E.132, N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 5 residues within 4Å: Chain B: E.458 Chain C: T.108, T.109, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 4 residues within 4Å: Chain B: K.551 Chain C: N.273, E.274, N.275 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 3 residues within 4Å: Chain C: N.609, T.611, Q.637 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 3 residues within 4Å: Chain C: N.710, T.712, Q.1064 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 3 residues within 4Å: Chain C: N.794, S.796, Q.797 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.6: 3 residues within 4Å: Chain A: A.699, E.1065, N.1067 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.699 NAG-NAG-FUC.16: 4 residues within 4Å: Chain B: A.699, E.1065, K.1066, N.1067 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.699 NAG-NAG-FUC.26: 3 residues within 4Å: Chain C: A.699, E.1065, N.1067 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-MAN.7: 4 residues within 4Å: Chain A: N.1091, T.1093, H.1094, F.1096 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.8: 2 residues within 4Å: Chain A: I.1125, N.1127 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.17: 4 residues within 4Å: Chain B: N.1091, T.1093, H.1094, F.1096 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.1096 NAG-NAG-MAN.18: 1 residues within 4Å: Chain B: N.1127 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.27: 4 residues within 4Å: Chain C: N.1091, T.1093, H.1094, F.1096 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.1096 NAG-NAG-MAN.28: 1 residues within 4Å: Chain C: N.1127 No protein-ligand interaction detected (PLIP)

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

NAG.29: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.30: 5 residues within 4Å: Chain A: N.122, T.124, N.125, V.127, E.154 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain A: K.147, N.149, S.151 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain A: E.132, N.165 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain A: N.273, N.275, T.277 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain A: N.336, V.360 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain A: N.596 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain A: N.650 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain A: N.702 Chain B: D.789 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain A: N.1151 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain B: K.147, N.148, N.149 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain B: N.234 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain B: N.324, T.326, Q.573 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain B: G.332, N.336 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain B: T.300, N.596 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain B: H.648, V.649, N.650 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain B: N.702, G.1124 Chain C: D.789 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain B: N.1151 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain C: Y.145, N.149 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain C: N.324, P.572, Q.573 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain C: N.596 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain C: N.650 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain A: D.789 Chain C: N.702 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain C: Y.1148, N.1151 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

2023-09-06

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein