SMTL ID : 7zh1.1

SARS CoV Spike protein, Closed C3 conformation

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: 7 residues within 4Å: Chain A: N.234 Chain B: R.451, H.452, G.453, K.454, R.456, E.459 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 7 residues within 4Å: Chain B: N.234 Chain C: R.451, H.452, G.453, K.454, R.456, E.459 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 7 residues within 4Å: Chain A: R.451, H.452, G.453, K.454, R.456, E.459 Chain C: N.234 No protein-ligand interaction detected (PLIP)

3 x EIC: LINOLEIC ACID(Non-covalent)

EIC.4: 11 residues within 4Å: Chain A: P.331, I.352, Y.359, Y.363, F.368, L.381, F.386, L.428 Chain B: R.402, Q.403, G.410 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.352, A:Y.359, A:F.368, A:L.381, A:F.386, A:F.386, A:L.428 Hydrogen bonds: A:Y.363, B:R.402, B:Q.403 EIC.15: 11 residues within 4Å: Chain B: P.331, I.352, Y.359, Y.363, F.368, L.381, F.386, L.428 Chain C: R.402, Q.403, G.410 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:I.352, B:Y.359, B:F.368, B:L.381, B:F.386, B:F.386, B:L.428 Hydrogen bonds: B:Y.363, C:R.402, C:Q.403 EIC.26: 11 residues within 4Å: Chain A: R.402, Q.403, G.410 Chain C: P.331, I.352, Y.359, Y.363, F.368, L.381, F.386, L.428 10 PLIP interactions: 2 interactions with chain A, 8 interactions with chain C Hydrogen bonds: A:R.402, A:Q.403, C:Y.363 Hydrophobic interactions: C:I.352, C:Y.359, C:F.368, C:L.381, C:F.386, C:F.386, C:L.428

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

NAG.5: 2 residues within 4Å: Chain A: N.116, E.138 Ligand excluded by PLIP NAG.6: 5 residues within 4Å: Chain A: N.126, S.127, T.128, N.129, V.131 Ligand excluded by PLIP NAG.7: 4 residues within 4Å: Chain A: F.164, N.165 Chain B: Y.345, A.346 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain A: N.276 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: N.325, P.572, K.573 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain A: N.364 Chain B: Y.449, Y.482 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: N.609 Chain C: M.823 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: N.706, Q.911, Q.1060 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: Y.785, N.790, S.792 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: E.1061, N.1063 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain B: N.116, E.138 Ligand excluded by PLIP NAG.17: 5 residues within 4Å: Chain B: N.126, S.127, T.128, N.129, V.131 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain B: F.164, N.165 Chain C: Y.345, A.346 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain B: N.276 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: N.325, P.572, K.573 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain B: N.364 Chain C: Y.449, Y.482 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: M.823 Chain B: N.609 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: N.706, Q.911, Q.1060 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: Y.785, N.790, S.792 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: E.1061, N.1063 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain C: N.116, E.138 Ligand excluded by PLIP NAG.28: 5 residues within 4Å: Chain C: N.126, S.127, T.128, N.129, V.131 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain A: Y.345, A.346 Chain C: F.164, N.165 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain C: N.276 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: N.325, P.572, K.573 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain A: Y.449 Chain C: N.364 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: M.823 Chain C: N.609 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: N.706, Q.911, Q.1060 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: Y.785, N.790, S.792 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: E.1061, N.1063 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Toelzer, C. et al., The free fatty acid-binding pocket is a conserved hallmark in pathogenic beta-coronavirus spike proteins from SARS-CoV to Omicron. Sci Adv (2022)

Release Date

2023-02-15

Peptides

Spike glycoprotein,Fibritin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein,Fibritin