SMTL ID : 6vxx.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

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: 5 residues within 4Å: Chain A: T.127, N.253, T.255 Chain C: K.481, E.484 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.736, L.941, Q.945 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.941 NAG-NAG.3: 3 residues within 4Å: Chain A: N.820, S.822, Q.823 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.1117, T.1119, H.1120, F.1122 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain A: N.1153 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain A: K.481, E.484 Chain B: T.127, N.253, T.255 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.736, L.941, Q.945 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.941 NAG-NAG.8: 3 residues within 4Å: Chain B: N.820, S.822, Q.823 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain B: N.1117, T.1119, H.1120, F.1122 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain B: N.1153 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain B: K.481, E.484 Chain C: T.127, N.253, T.255 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain C: N.736, L.941, Q.945 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.941 NAG-NAG.13: 3 residues within 4Å: Chain C: N.820, S.822, Q.823 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain C: N.1117, T.1119, H.1120, F.1122 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 1 residues within 4Å: Chain C: N.1153 No protein-ligand interaction detected (PLIP)

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

NAG.16: 1 residues within 4Å: Chain A: N.80 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: N.141, A.142, N.144, K.148 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: N.299, E.300, N.301 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain A: P.349, N.350, P.598, Q.599 Ligand excluded by PLIP NAG.20: 6 residues within 4Å: Chain A: F.357, G.358, F.361, N.362, V.386, L.387 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.622 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: N.635, Q.663 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: H.674, N.676 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: N.728, I.1149, G.1150 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain A: A.725, E.1091, K.1092, N.1093 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: E.151, N.184 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.80 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain B: N.141, A.142, N.144, K.148 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: N.299, E.300, N.301 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain B: P.349, N.350, P.598, Q.599 Ligand excluded by PLIP NAG.31: 6 residues within 4Å: Chain B: F.357, G.358, F.361, N.362, V.386, L.387 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.622 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: N.635, Q.663 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: H.674, N.676 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: N.728, I.1149, G.1150 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain B: A.725, E.1091, K.1092, N.1093 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: E.151, N.184 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain C: N.80 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain C: N.141, A.142, N.144, K.148 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: N.299, E.300, N.301 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain C: P.349, N.350, P.598, Q.599 Ligand excluded by PLIP NAG.42: 6 residues within 4Å: Chain C: F.357, G.358, F.361, N.362, V.386, L.387 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain C: N.622 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: N.635, Q.663 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: H.674, N.676 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain C: N.728, I.1149, G.1150 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain C: A.725, E.1091, K.1092, N.1093 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain C: E.151, N.184 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Walls, A.C. et al., Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein. Cell (2020)

Release Date

2020-03-11

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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