SMTL ID : 7e9t.1

Nanometer resolution in situ structure of SARS-CoV-2 post-fusion spike

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

3 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: K.489, N.492 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain B: K.489, N.492 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain C: K.489, N.492 No protein-ligand interaction detected (PLIP)

9 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: 2 residues within 4Å: Chain A: N.456 Chain C: E.46 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.3: 7 residues within 4Å: Chain A: N.432, T.434, D.437 Chain C: I.24, R.312, P.355, H.356 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.312 NAG-NAG-MAN.5: 2 residues within 4Å: Chain A: E.46 Chain B: N.456 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.6: 8 residues within 4Å: Chain A: I.24, R.312, A.354, P.355, H.356 Chain B: N.432, T.434, D.437 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.312 NAG-NAG-MAN.8: 2 residues within 4Å: Chain B: E.46 Chain C: N.456 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.9: 7 residues within 4Å: Chain B: I.24, R.312, P.355, H.356 Chain C: N.432, T.434, D.437 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.312 NAG-NAG-MAN.10: 3 residues within 4Å: Chain B: N.396, F.401, P.410 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.11: 3 residues within 4Å: Chain C: N.396, G.397, F.401 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.12: 3 residues within 4Å: Chain A: N.396, F.401, P.410 No protein-ligand interaction detected (PLIP)

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

NAG.13: 1 residues within 4Å: Chain A: N.471 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.471 NAG.14: 4 residues within 4Å: Chain A: N.7, T.374, S.395, W.400 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.395 NAG.15: 2 residues within 4Å: Chain A: N.15, Q.369 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.15, A:Q.369 NAG.16: 1 residues within 4Å: Chain B: N.471 No protein-ligand interaction detected (PLIP) NAG.17: 4 residues within 4Å: Chain B: N.7, T.374, S.395, W.400 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.395 NAG.18: 2 residues within 4Å: Chain B: N.15, Q.369 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.15, B:Q.369 NAG.19: 1 residues within 4Å: Chain C: N.471 No protein-ligand interaction detected (PLIP) NAG.20: 4 residues within 4Å: Chain C: N.7, T.374, S.395, W.400 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.395 NAG.21: 2 residues within 4Å: Chain C: N.15, Q.369 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.15, C:Q.369

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tai, L. et al., Nanometer-resolution in situ structure of the SARS-CoV-2 postfusion spike protein. Proc.Natl.Acad.Sci.USA (2021)

Release Date

2021-11-17

Peptides

Spike protein S2: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

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