SMTL ID : 6zb5.1

SARS CoV-2 Spike protein, Closed conformation, C3 symmetry

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(Non-covalent)(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain A: N.717, L.922, Q.926 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.922 NAG-NAG.2: 2 residues within 4Å: Chain B: N.717, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain C: N.717, L.922, Q.926 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.922

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

NAG.4: 2 residues within 4Å: Chain A: N.343, S.371 Ligand excluded by PLIP NAG.5: 5 residues within 4Å: Chain A: N.164, N.165 Chain B: Y.351, A.352, I.468 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain A: N.616, Q.644 Chain C: I.834 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: N.801, S.803 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain A: E.1072, N.1074 Chain C: Q.895 Ligand excluded by PLIP NAG.9: 5 residues within 4Å: Chain A: T.108, N.234 Chain B: R.457, N.460, E.465 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain B: N.801, S.803 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain B: N.343, S.371 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain B: N.164, N.165 Chain C: Y.351 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: I.834 Chain B: N.616, Q.644 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain B: 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, T.236 Chain C: R.457, S.459, N.460, K.462 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain B: C.15, N.17, N.137 Ligand excluded by PLIP NAG.21: 6 residues within 4Å: Chain A: R.457, S.459, N.460 Chain C: T.108, N.234, T.236 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain C: N.343, S.371 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: Y.351 Chain C: N.164, N.165 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain C: N.616, Q.644 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain C: N.801, S.803 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain C: E.1072, N.1074 Ligand excluded by PLIP

3 x EIC: LINOLEIC ACID(Non-covalent)

EIC.10: 9 residues within 4Å: Chain A: R.408 Chain C: A.363, Y.365, F.374, F.377, F.392, V.395, L.513, F.515 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:A.363, C:Y.365, C:F.374, C:F.392, C:V.395, C:L.513, C:F.515 Salt bridges: A:R.408 EIC.19: 11 residues within 4Å: Chain A: F.338, A.363, Y.369, F.377, L.387, F.392, L.513, F.515 Chain B: Q.409, G.416, K.417 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.338, A:A.363, A:F.377, A:F.377, A:L.387, A:F.392, A:L.513, A:F.515 Hydrogen bonds: B:Q.409, B:K.417 EIC.20: 11 residues within 4Å: Chain B: F.338, I.358, Y.365, Y.369, F.374, F.377, L.387, F.392, V.395 Chain C: T.415, G.416 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.338, B:I.358, B:Y.365, B:Y.365, B:Y.365, B:F.374, B:F.377, B:L.387, B:F.392, B:V.395

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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