SMTL ID : 7lws.1

UK (B.1.1.7) SARS-CoV-2 S-GSAS-D614G variant spike protein in the 3-RBD-down conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

18 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: 3 residues within 4Å: Chain A: N.706, G.1128 Chain B: D.793 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 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.3: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.1071, F.1072, T.1073 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100, Y.1107 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain A: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain B: N.706, G.1128 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain B: N.714, L.919, Q.923, Q.1068 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.919 NAG-NAG.9: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain B: A.703, N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain B: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain C: N.706, P.1076, G.1128 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain C: N.714, L.919, Q.923, Q.1068 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.919 NAG-NAG.15: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain C: S.701, A.703, E.1069, N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 1 residues within 4Å: Chain C: N.1131 No protein-ligand interaction detected (PLIP)

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

NAG.19: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: E.130, F.131, N.162 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: T.106, N.231 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: N.277, N.279 Chain C: K.555 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: N.328, P.576, Q.577 Ligand excluded by PLIP NAG.24: 5 residues within 4Å: Chain A: N.340, S.368, S.370, F.371, W.433 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: N.600, T.601 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: N.613, T.615 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain A: H.652, N.654 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: E.130, N.162 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: T.106, N.231 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: E.278, N.279 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: G.336, N.340 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: T.599, N.600 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: N.613, T.615 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain B: H.652, N.654 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: N.328, Q.577 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain B: N.120, N.123, V.125, V.168 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain B: K.459 Chain C: T.106, N.231 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: N.277, N.279 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: N.328, Q.577 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: G.336, N.340, L.365 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain C: N.600 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: N.613, T.615 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain C: N.654, N.655, T.693 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. Biorxiv (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

Related Entries With Identical Sequence