SMTL ID : 7ybm.1

SARS-CoV-2 C.1.2 variant spike (Close state)

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: 2 residues within 4Å: Chain A: C.15, N.17 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.164, N.165 Chain B: Y.349, I.466 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: N.614, T.616, Q.642 Chain C: Q.834 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain B: C.15, N.17 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 5 residues within 4Å: Chain B: E.132, N.164, N.165 Chain C: Y.349, I.466 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain A: Q.834 Chain B: N.614, T.616 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 2 residues within 4Å: Chain C: C.15, N.17 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 5 residues within 4Å: Chain A: Y.349, I.466 Chain C: E.132, N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 3 residues within 4Å: Chain B: Q.834 Chain C: N.614, T.616 No protein-ligand interaction detected (PLIP)

21 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.2: 4 residues within 4Å: Chain A: N.122, T.124, V.127, E.169 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.4: 9 residues within 4Å: Chain A: T.108, N.234, T.236 Chain B: R.455, K.456, S.457, N.458, L.459, K.460 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.5: 3 residues within 4Å: Chain A: N.278, E.279, N.280 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.7: 5 residues within 4Å: Chain A: N.715, F.716, T.717, L.920, Q.924 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.924 NAG-NAG-MAN.8: 4 residues within 4Å: Chain A: N.799, S.801, Q.802, F.815 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.815 NAG-NAG-MAN.10: 4 residues within 4Å: Chain A: N.1096, T.1098, H.1099, F.1101 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.11: 1 residues within 4Å: Chain A: N.1132 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.13: 4 residues within 4Å: Chain B: N.122, T.124, N.125, V.127 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.15: 8 residues within 4Å: Chain B: T.108, N.234, T.236 Chain C: R.455, K.456, S.457, N.458, L.459 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.16: 2 residues within 4Å: Chain B: E.279, N.280 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.18: 3 residues within 4Å: Chain B: N.715, L.920, Q.924 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Q.924 NAG-NAG-MAN.19: 3 residues within 4Å: Chain B: N.799, S.801, Q.802 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.21: 3 residues within 4Å: Chain B: N.1096, H.1099, F.1101 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.22: 1 residues within 4Å: Chain B: N.1132 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.24: 4 residues within 4Å: Chain C: N.122, T.124, N.125, V.127 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.26: 8 residues within 4Å: Chain A: R.455, K.456, S.457, N.458, L.459 Chain C: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.27: 3 residues within 4Å: Chain C: N.278, E.279, N.280 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.29: 5 residues within 4Å: Chain C: N.715, T.717, L.920, Q.924, Q.1069 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.920, C:Q.924 NAG-NAG-MAN.30: 3 residues within 4Å: Chain C: N.799, S.801, Q.802 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.32: 3 residues within 4Å: Chain C: N.1096, H.1099, F.1101 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.33: 1 residues within 4Å: Chain C: N.1132 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.9: 4 residues within 4Å: Chain A: S.702, A.704, E.1070, N.1072 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.704 NAG-NAG-FUC.20: 4 residues within 4Å: Chain B: S.702, A.704, E.1070, N.1072 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.704 NAG-NAG-FUC.31: 4 residues within 4Å: Chain C: S.702, A.704, E.1070, N.1072 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:A.704

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

NAG.34: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain A: K.147, N.149, M.153 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain A: N.329, Q.578, T.579 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain A: F.336, G.337, F.340, N.341 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain A: N.601 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain A: Y.653, N.655 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain A: N.707, G.1129 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain A: N.1156 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain B: K.147, N.148, N.149 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain B: N.329 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain B: F.336, G.337, F.340, N.341 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain B: N.601 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain B: Y.653, N.655 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain B: N.707, G.1129 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain B: N.1156 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain C: K.147, N.148, N.149, M.153 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain C: N.329, P.577 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain C: F.336, G.337, F.340, N.341 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain C: N.601 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain C: Y.653, N.655 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain C: N.707, G.1129 Ligand excluded by PLIP NAG.57: 1 residues within 4Å: Chain C: N.1156 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

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