SMTL ID : 6zb4.1

SARS CoV-2 Spike protein, Closed conformation, C1 symmetry

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

1 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: 3 residues within 4Å: Chain A: N.717, L.922, Q.926 No protein-ligand interaction detected (PLIP)

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

NAG.2: 5 residues within 4Å: Chain A: F.338, G.339, N.343, L.368, S.371 Ligand excluded by PLIP NAG.3: 3 residues within 4Å: Chain A: N.164, N.165 Chain B: I.468 Ligand excluded by PLIP NAG.4: 4 residues within 4Å: Chain A: N.616, Q.644 Chain C: F.833, I.834 Ligand excluded by PLIP NAG.5: 2 residues within 4Å: Chain A: N.801, S.803 Ligand excluded by PLIP NAG.6: 1 residues within 4Å: Chain A: N.1074 Ligand excluded by PLIP NAG.7: 5 residues within 4Å: Chain A: T.108, N.234, T.236 Chain B: R.457, S.459 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain B: N.717, Q.926 Ligands: NAG.10 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain B: L.922 Ligands: NAG.9 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain B: G.339, N.343, S.371 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain B: N.164, N.165 Chain C: I.468 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain A: I.834 Chain B: N.616, T.645, R.646 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain B: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain B: E.281, N.282 Ligand excluded by PLIP NAG.17: 7 residues within 4Å: Chain B: T.108, N.234 Chain C: R.457, S.459, N.460, K.462, E.465 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain B: N.17 Ligand excluded by PLIP NAG.20: 6 residues within 4Å: Chain A: R.457, N.460, K.462 Chain C: T.108, N.234, T.236 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain C: N.717, Q.926 Ligands: NAG.22 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain C: L.922 Ligands: NAG.21 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain C: F.338, N.343, V.367, S.371 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain C: N.164, N.165 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain C: N.616 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain C: N.1074 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain C: C.15, N.17, N.137 Ligand excluded by PLIP

3 x EIC: LINOLEIC ACID(Non-covalent)

EIC.8: 10 residues within 4Å: Chain A: F.338, I.358, Y.365, Y.369, F.374, F.377, L.387, F.392, V.395, L.513 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.338, A:I.358, A:Y.365, A:F.374, A:F.377, A:L.387, A:F.392, A:V.395, A:L.513 EIC.19: 7 residues within 4Å: Chain B: F.338, A.363, Y.365, Y.369, F.374, L.387 Chain C: Q.409 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:F.338, B:F.338, B:A.363, B:Y.365, B:Y.365, B:Y.369, B:L.387 Hydrogen bonds: C:Q.409, C:K.417 EIC.29: 11 residues within 4Å: Chain A: R.408 Chain C: F.338, I.358, A.363, Y.365, Y.369, F.374, F.377, L.387, F.392, L.513 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:F.338, C:I.358, C:A.363, C:Y.365, C:Y.365, C:Y.365, C:Y.369, C:F.374, C:F.374, C:F.377, C:L.387, C:F.392

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Toelzer, C. et al., Free fatty acid binding pocket in the locked structure of SARS-CoV-2 spike protein. Science (2020)

Release Date

2020-09-30

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
B

C
A

Spike glycoprotein

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