SMTL ID : 7edg.1

Cryo-EM structure of SARS-CoV-2 S-UK variant (B.1.1.7), one RBD-up conformation 2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

29 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.126, T.128, V.131 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 1 residues within 4Å: Chain A: N.285 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.334, Q.583, T.584 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: F.341, G.342, N.346, V.370 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: N.619, Q.647 Chain B: R.850, L.852 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.850, B:R.850 NAG-NAG.7: 3 residues within 4Å: Chain A: N.712, G.1134 Chain B: D.799 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain A: N.720, Q.929, Q.1074 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.929 NAG-NAG.9: 3 residues within 4Å: Chain A: N.804, S.806, Q.807 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain A: S.707, A.709, E.1075, N.1077 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.709 NAG-NAG.11: 3 residues within 4Å: Chain A: N.1101, H.1104, F.1106 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain A: N.1137 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain A: K.561 Chain B: N.283, E.284, N.285 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain B: F.341, G.342, F.345, N.346 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 5 residues within 4Å: Chain B: N.619, R.649 Chain C: R.850, L.852, I.853 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.850, C:R.850 NAG-NAG.16: 3 residues within 4Å: Chain B: S.711, N.712, N.713 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 2 residues within 4Å: Chain B: N.720, Q.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain B: N.804, S.806, Q.807 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 4 residues within 4Å: Chain B: S.707, A.709, E.1075, N.1077 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.707 NAG-NAG.20: 4 residues within 4Å: Chain B: N.1101, T.1103, H.1104, F.1106 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 1 residues within 4Å: Chain B: N.1137 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 4 residues within 4Å: Chain B: K.561 Chain C: N.283, E.284, N.285 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 2 residues within 4Å: Chain C: F.345, N.346 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.376, C:S.376 NAG-NAG.24: 3 residues within 4Å: Chain A: I.853 Chain C: N.619, T.621 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 4 residues within 4Å: Chain A: D.799 Chain C: S.711, N.712, N.713 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 3 residues within 4Å: Chain C: N.720, L.925, Q.1074 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.925 NAG-NAG.27: 2 residues within 4Å: Chain C: N.804, S.806 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 5 residues within 4Å: Chain C: S.707, V.708, A.709, E.1075, N.1077 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.707, C:A.709 NAG-NAG.29: 4 residues within 4Å: Chain C: N.1101, T.1103, H.1104, F.1106 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 1 residues within 4Å: Chain C: N.1137 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.2: 2 residues within 4Å: Chain A: T.112, N.237 No protein-ligand interaction detected (PLIP)

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

NAG.31: 3 residues within 4Å: Chain A: Y.34, F.65, N.67 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain A: N.167, N.168 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain A: N.606 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain A: H.658, N.660 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain B: Y.34, N.67 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain B: V.124, N.125, N.126 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: N.167, N.168 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain B: G.235, I.236, N.237 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain B: N.334, P.582, Q.583 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain B: N.606, T.607 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain B: N.660 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: Y.34, N.36, N.67 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain C: N.126, T.128, V.131 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain C: S.116, E.136, N.167, N.168 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: N.237, T.239 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain C: N.334, Q.583 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: N.606, T.607 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain C: N.660 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, T.J. et al., Effect of SARS-CoV-2 B.1.1.7 mutations on spike protein structure and function. Nat.Struct.Mol.Biol. (2021)

Release Date

2021-09-01

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