SMTL ID : 7ybi.1

SARS-CoV-2 Mu variant spike (open state)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 4.10 Å

Oligo State

homo-trimer

Ligands

20 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: 3 residues within 4Å: Chain A: N.331, Q.580, L.582 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: N.616, T.618 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: N.801, S.803 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: 3 residues within 4Å: Chain B: N.122, T.124, V.127 No protein-ligand interaction detected (PLIP) 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.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain B: N.616, T.618 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain B: N.717, L.922, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 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: 2 residues within 4Å: Chain C: N.122, T.124 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain C: E.132, N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 5 residues within 4Å: Chain B: E.465 Chain C: T.108, N.234, T.236, R.237 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:T.236 NAG-NAG.23: 4 residues within 4Å: Chain B: K.558 Chain C: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 2 residues within 4Å: Chain C: N.616, T.618 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 4 residues within 4Å: Chain C: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 2 residues within 4Å: Chain C: N.801, Q.804 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.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.16: 4 residues within 4Å: Chain B: A.706, E.1072, K.1073, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.27: 4 residues within 4Å: Chain C: A.706, E.1072, K.1073, N.1074 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.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.8: 2 residues within 4Å: Chain A: I.1132, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.17: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.18: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.28: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.29: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP)

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

NAG.30: 3 residues within 4Å: Chain A: Y.28, F.59, N.61 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain A: N.122, T.124, N.125, V.127 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain A: K.147, N.149, S.151 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain A: E.132, N.164, N.165 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain A: N.234 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain A: N.282 Chain C: K.558 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain A: G.339, F.342, N.343 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain A: N.709, G.1131 Chain B: D.796 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain A: N.1158 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain B: K.147, N.148, N.149 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain B: G.232, N.234 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain B: F.338, G.339, F.342, N.343 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain B: H.655, V.656, N.657 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain B: N.709, G.1131 Chain C: D.796 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain B: Y.1155, N.1158 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain C: N.145, N.148, N.149 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain C: P.330, N.331, I.332, Q.580 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain C: G.339, F.342, N.343 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.55: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain A: D.796 Chain C: N.709 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain C: Y.1155, N.1158 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

2023-07-12

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein