SMTL ID : 8fdw.1

Cryo-EM structure of SARS-CoV-2 postfusion spike in membrane

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

6 x NAG- NAG- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN-MAN.1: 4 residues within 4Å: Chain A: N.413, H.416, F.418 Ligands: MAN.16 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN-MAN.2: 4 residues within 4Å: Chain A: N.449, T.451, D.454 Chain B: I.41 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN-MAN.6: 4 residues within 4Å: Chain B: N.413, H.416, F.418 Ligands: MAN.20 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN-MAN.7: 4 residues within 4Å: Chain B: N.449, T.451, D.454 Chain C: I.41 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN-MAN.11: 4 residues within 4Å: Chain C: N.413, H.416, F.418 Ligands: MAN.24 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN-MAN.12: 4 residues within 4Å: Chain A: I.41 Chain C: N.449, T.451, D.454 No protein-ligand interaction detected (PLIP)

3 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.3: 3 residues within 4Å: Chain A: K.464, N.473 Chain B: D.300 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.8: 2 residues within 4Å: Chain B: K.464, N.473 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.13: 2 residues within 4Å: Chain C: K.464, N.473 No protein-ligand interaction detected (PLIP)

6 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.4: 2 residues within 4Å: Chain A: S.26, N.389 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.509, L.512 Chain B: Q.250 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain B: S.26, N.389 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain B: N.509, L.512 Chain C: Q.250 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain C: S.26, N.389 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain A: Q.250 Chain C: N.509, L.512 No protein-ligand interaction detected (PLIP)

3 x MAN: alpha-D-mannopyranose(Non-functional Binders)

MAN.16: 1 residues within 4Å: Ligands: NAG-NAG-MAN-MAN.1 No protein-ligand interaction detected (PLIP) MAN.20: 1 residues within 4Å: Ligands: NAG-NAG-MAN-MAN.6 No protein-ligand interaction detected (PLIP) MAN.24: 1 residues within 4Å: Ligands: NAG-NAG-MAN-MAN.11 No protein-ligand interaction detected (PLIP)

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

NAG.17: 4 residues within 4Å: Chain A: Y.22, N.24, I.396, W.417 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.396 NAG.18: 5 residues within 4Å: Chain A: T.31, N.32, F.424 Chain C: K.401, G.439 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:F.424 Hydrogen bonds: A:N.32, C:K.401 NAG.19: 2 residues within 4Å: Chain A: G.486, N.488 No protein-ligand interaction detected (PLIP) NAG.21: 4 residues within 4Å: Chain B: Y.22, N.24, I.396, W.417 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.396 NAG.22: 5 residues within 4Å: Chain A: K.401, G.439 Chain B: T.31, N.32, F.424 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.401, B:N.32 Hydrophobic interactions: B:F.424 NAG.23: 3 residues within 4Å: Chain A: Q.269 Chain B: G.486, N.488 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.269 NAG.25: 4 residues within 4Å: Chain C: Y.22, N.24, I.396, W.417 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.396 Hydrogen bonds: C:N.24 NAG.26: 5 residues within 4Å: Chain B: K.401, G.439 Chain C: T.31, N.32, F.424 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:F.424 Hydrogen bonds: C:N.32, B:K.401 NAG.27: 3 residues within 4Å: Chain B: Q.269 Chain C: G.486, N.488 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.269

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shi, W. et al., Cryo-EM structure of SARS-CoV-2 postfusion spike in membrane. Nature (2023)

Release Date

2023-05-10

Peptides

Spike protein S2: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
C

Membrane

We predict this structure to be a membrane protein.
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Spike protein S2