SMTL ID : 7fce.1

Structure of the SARS-CoV-2 A372T spike glycoprotein (closed)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

27 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: Y.28, N.61 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: N.122, T.124, N.125, V.127, V.171 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain A: E.132, N.164, N.165 Chain C: Y.351, A.352 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 9 residues within 4Å: Chain A: T.108, N.234, T.236 Chain C: R.457, K.458, S.459, N.460, K.462, E.465 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain B: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain B: N.122, T.124, N.125, V.127, V.171 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 5 residues within 4Å: Chain A: Y.351, A.352 Chain B: E.132, N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 9 residues within 4Å: Chain A: R.457, K.458, S.459, N.460, K.462, E.465 Chain B: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain B: N.616, Q.644 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain B: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain C: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 5 residues within 4Å: Chain C: N.122, T.124, N.125, V.127, V.171 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 5 residues within 4Å: Chain B: Y.351, A.352 Chain C: E.132, N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 9 residues within 4Å: Chain B: R.457, K.458, S.459, N.460, K.462, E.465 Chain C: T.108, N.234, T.236 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.458 NAG-NAG.23: 2 residues within 4Å: Chain C: N.616, Q.644 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 4 residues within 4Å: Chain C: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP)

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

NAG.28: 3 residues within 4Å: Chain A: N.280, E.281, N.282 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain A: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain A: N.343, S.371 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain A: N.709, I.1130, G.1131 Chain B: D.796 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain A: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.34: 5 residues within 4Å: Chain A: N.370 Chain C: L.455, F.456, Y.489, Q.493 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain A: N.616, Q.644 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain B: N.280, E.281, N.282 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain B: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain B: N.343, S.371 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain B: N.709, I.1130, G.1131 Chain C: D.796 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain B: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain A: L.455, F.456, Q.493 Chain B: N.370 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain C: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain C: N.343, S.371 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain A: D.796 Chain C: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain C: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.50: 5 residues within 4Å: Chain B: Y.453, L.455, F.456, Q.493 Chain C: N.370 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, S. et al., Loss of Spike N370 glycosylation as an important evolutionary event for the enhanced infectivity of SARS-CoV-2. Cell Res. (2022)

Release Date

2022-01-26

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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