SMTL ID : 7edi.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

31 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: 8 residues within 4Å: Chain A: V.124, N.126, T.128, V.131, E.157, F.160, E.172, V.174 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.172 NAG-NAG.2: 4 residues within 4Å: Chain A: N.283, E.284, N.285 Chain C: K.561 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.334, Q.583, T.584, L.585 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.619, T.621, Q.647 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain A: N.712 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: N.720, L.925, Q.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: N.804, S.806, Q.807 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain A: S.707, A.709, E.1075, K.1076, N.1077 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.707 NAG-NAG.9: 4 residues within 4Å: Chain A: N.1101, T.1103, H.1104, F.1106 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain A: I.1135, N.1137 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 6 residues within 4Å: Chain B: N.126, T.128, N.129, V.131, K.133, E.172 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.131 NAG-NAG.12: 3 residues within 4Å: Chain A: K.561 Chain B: E.284, N.285 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.561 NAG-NAG.13: 4 residues within 4Å: Chain B: F.341, G.342, F.345, N.346 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain B: N.619, Q.647 Chain C: R.850 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain B: N.712, I.1133 Chain C: D.799 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 2 residues within 4Å: Chain B: N.720, Q.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain B: N.804, S.806, Q.807 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain B: S.707, A.709, N.1077 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.709 NAG-NAG.19: 3 residues within 4Å: Chain B: N.1101, H.1104, F.1106 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 1 residues within 4Å: Chain B: N.1137 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain C: T.112, N.237, T.239 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 3 residues within 4Å: Chain B: K.561 Chain C: E.284, N.285 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain C: N.334, P.582, Q.583, T.584 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.584 NAG-NAG.24: 6 residues within 4Å: Chain C: F.341, G.342, N.346, V.370, N.373, S.374 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 5 residues within 4Å: Chain A: D.851, L.852, I.853 Chain C: N.619, R.649 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 3 residues within 4Å: Chain A: D.799 Chain C: N.712, G.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 2 residues within 4Å: Chain C: N.720, Q.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 2 residues within 4Å: Chain C: N.804, S.806 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 5 residues within 4Å: Chain A: Q.898 Chain C: S.707, A.709, E.1075, N.1077 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:A.709 NAG-NAG.30: 2 residues within 4Å: Chain C: N.1101, H.1104 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 1 residues within 4Å: Chain C: N.1137 No protein-ligand interaction detected (PLIP)

16 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.32: 4 residues within 4Å: Chain A: Y.34, F.65, S.66, N.67 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain A: N.168, T.170 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain A: G.235, N.237 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain A: N.606, T.607 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain A: H.658, N.660 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain B: Y.34, N.36, S.66, N.67 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain B: N.168 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain B: G.235, N.237 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain B: N.334, Q.583 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain B: N.606 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain B: H.658, N.660 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: Y.34, N.67 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain C: N.126 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: N.167, N.168 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain C: N.606 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: H.658, 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

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