SMTL ID : 7odl.1

SARS CoV-2 Spike protein, Bristol UK Deletion variant, Closed conformation, C1 symmetry

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

3 x EIC: LINOLEIC ACID(Non-covalent)

EIC.1: 13 residues within 4Å: Chain A: F.338, V.341, A.363, Y.365, Y.369, F.374, F.377, L.387, F.392, V.395, I.434, L.513 Chain C: G.416 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.341, A:Y.365, A:F.377, A:L.387, A:F.392, A:V.395, A:I.434, A:L.513, A:L.513 EIC.12: 13 residues within 4Å: Chain A: G.416 Chain B: I.358, A.363, Y.365, Y.369, F.374, F.377, L.387, F.392, V.395, I.434, L.513, V.524 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:I.358, B:A.363, B:Y.365, B:F.374, B:F.377, B:L.387, B:F.392, B:F.392, B:V.395, B:I.434, B:L.513, B:L.513, B:V.524 Hydrogen bonds: B:Y.369 EIC.23: 12 residues within 4Å: Chain B: R.408, T.415, G.416 Chain C: F.338, V.341, A.363, Y.365, F.377, L.387, F.392, V.395, L.513 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:V.341, C:Y.365, C:Y.365, C:F.377, C:L.387, C:F.392, C:V.395, C:L.513 Hydrogen bonds: B:R.408

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

NAG.2: 1 residues within 4Å: Chain A: N.1126 Ligand excluded by PLIP NAG.3: 4 residues within 4Å: Chain A: N.164, N.165 Chain C: Y.351, I.468 Ligand excluded by PLIP NAG.4: 7 residues within 4Å: Chain A: T.108, N.234 Chain C: R.457, S.459, N.460, K.462, E.465 Ligand excluded by PLIP NAG.5: 2 residues within 4Å: Chain A: E.281, N.282 Ligand excluded by PLIP NAG.6: 2 residues within 4Å: Chain A: N.343, S.371 Ligand excluded by PLIP NAG.7: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain A: N.701, N.702, G.1123 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: N.709, L.914, Q.1063 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain A: N.793, S.795, Q.796 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: E.1064, N.1066 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain A: Y.351, I.468 Chain B: N.164, N.165 Ligand excluded by PLIP NAG.14: 8 residues within 4Å: Chain A: R.457, S.459, N.460, K.462, E.465 Chain B: T.108, N.234, T.236 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain B: E.281, N.282 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain B: N.343, S.371 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain B: N.616 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: N.701, G.1123 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain B: N.709 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: N.793, S.795, Q.796 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain B: E.1064, K.1065, N.1066 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: V.1125, N.1126 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain C: N.164, N.165 Ligand excluded by PLIP NAG.25: 7 residues within 4Å: Chain B: R.457, S.459, N.460, K.462, E.465 Chain C: T.108, N.234 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: K.558 Chain C: E.281, N.282 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain C: N.343, S.371 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain A: I.826 Chain C: N.616, Q.644 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain C: N.701, N.702, G.1123 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain C: N.709, Q.1063 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: N.793, S.795, Q.796 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: E.1064, N.1066 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain C: N.1126 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gupta, K. et al., Structural insights in cell-type specific evolution of intra-host diversity by SARS-CoV-2. Nat Commun (2022)

Release Date

2022-01-26

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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