SMTL ID : 7zh2.1

SARS CoV Spike protein, Closed C1 conformation

Coordinates

PDB Format

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: 5 residues within 4Å: Chain A: S.92, N.214 Chain B: R.431, H.432, K.434 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 7 residues within 4Å: Chain B: S.92, N.214, T.216 Chain C: R.431, H.432, K.434, R.436 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain A: R.431, H.432, R.436 Chain C: S.92, N.214, T.216 No protein-ligand interaction detected (PLIP)

3 x EIC: LINOLEIC ACID(Non-covalent)

EIC.4: 11 residues within 4Å: Chain A: C.310, P.311, V.315, I.332, A.337, Y.339, Y.343, F.366, V.369, L.408, L.486 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:P.311, A:V.315, A:I.332, A:A.337, A:Y.339, A:Y.339, A:F.366, A:V.369, A:L.408, A:L.486 EIC.14: 9 residues within 4Å: Chain B: P.311, F.312, V.315, I.332, A.337, Y.339, F.348, F.366, V.369 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:P.311, B:F.312, B:V.315, B:I.332, B:A.337, B:Y.339, B:Y.339, B:F.348, B:F.366, B:V.369 Hydrogen bonds: B:Y.339 EIC.24: 14 residues within 4Å: Chain C: P.311, F.312, V.315, A.337, Y.339, Y.343, F.348, F.351, L.361, F.366, V.369, L.408, L.486, F.488 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:P.311, C:F.312, C:F.312, C:V.315, C:A.337, C:Y.339, C:Y.339, C:F.348, C:L.361, C:F.366, C:F.366, C:V.369, C:L.408, C:L.486, C:F.488 Hydrogen bonds: C:Y.339

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

NAG.5: 3 residues within 4Å: Chain A: N.96, E.118, F.144 Ligand excluded by PLIP NAG.6: 5 residues within 4Å: Chain A: N.106, S.107, T.108, N.109, V.111 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: F.144, N.145 Ligand excluded by PLIP NAG.8: 4 residues within 4Å: Chain A: D.254, E.255, N.256 Chain B: R.531 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: N.305, K.553 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain A: N.344 Chain B: Y.429, Y.462 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: N.589 Chain C: M.803, Q.805 Ligand excluded by PLIP NAG.12: 4 residues within 4Å: Chain A: Y.765, N.770, S.772, Q.773 Ligand excluded by PLIP NAG.13: 6 residues within 4Å: Chain A: N.686, F.687, N.888, Q.891, Q.1040, F.1078 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain B: N.96, F.144 Ligands: NAG.17 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain B: N.106, T.108, N.109 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain B: F.144, N.145 Chain C: A.326 Ligands: NAG.15 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: E.255, N.256 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: N.305, K.553 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: N.344 Chain C: Y.429, Y.462 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain B: N.589 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain B: Y.765, N.770, S.772, Q.773 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: T.685, N.686, F.1078 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain C: N.96, E.118, F.144 Ligand excluded by PLIP NAG.26: 6 residues within 4Å: Chain C: N.106, S.107, T.108, N.109, V.111, I.151 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain C: N.145 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain A: R.531 Chain C: E.255, N.256 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain C: N.305, K.553 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain A: Y.429, Y.462 Chain C: N.344 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: M.803 Chain C: N.589 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain C: Y.765, N.770, S.772 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain C: T.685, N.686, Q.891, Q.1040 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

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