SMTL ID : 7lwt.1

UK (B.1.1.7) SARS-CoV-2 spike protein variant (S-GSAS-B.1.1.7) in the 1-RBD-up conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

9 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: 1 residues within 4Å: Chain A: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.714, L.919, Q.923, Q.1068 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.919 NAG-NAG.4: 1 residues within 4Å: Chain B: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain B: N.714, L.919, N.922, Q.923, Q.1068 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.919 Hydrogen bonds: B:N.922 NAG-NAG.7: 3 residues within 4Å: Chain B: N.328, P.576, Q.577 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain C: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain C: N.714, L.919, Q.923, Q.1068 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.919, C:Q.923 Hydrogen bonds: C:N.922

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

NAG.10: 2 residues within 4Å: Chain A: E.1069, N.1071 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: N.706, G.1128 Chain B: D.793 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: N.613, T.615 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: F.335, G.336, N.340 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.279 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.231 Chain C: K.459 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.61 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: H.652, N.654 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: N.328, Q.577, T.578 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: E.1069, N.1071 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: N.706, I.1127, G.1128 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: H.652, N.654 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: N.613, T.615 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain B: F.335, G.336, F.339, N.340 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: N.277, E.278, N.279 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: T.106, N.231 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain C: A.703, E.1069, N.1071 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain C: N.706, G.1128 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain C: N.654 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain C: N.613, T.615, Q.641 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: N.600, T.601 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: G.336, N.340, L.365 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain C: N.328, Q.577, L.579 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: N.277, N.279 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain C: N.231 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gobeil, S.M. et al., Effect of natural mutations of SARS-CoV-2 on spike structure, conformation, and antigenicity. Science (2021)

Release Date

2021-03-31

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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