SMTL ID : 7xy4.1

Cryo-EM structure of SARS-CoV-2 spike in complex with VHH21

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: Y.15, N.17, N.48 Ligand excluded by PLIP NAG.2: 2 residues within 4Å: Chain A: N.221, T.223 Ligand excluded by PLIP NAG.3: 3 residues within 4Å: Chain A: N.267, E.268, N.269 Ligand excluded by PLIP NAG.4: 2 residues within 4Å: Chain A: N.318, Q.567 Ligand excluded by PLIP NAG.5: 4 residues within 4Å: Chain A: F.325, G.326, F.329, N.330 Ligand excluded by PLIP NAG.6: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: H.642, N.644 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: N.696 Chain B: D.783 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: A.693, E.1059, N.1061 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain A: N.704, Q.913, Q.1058 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: N.788, S.790, Q.791 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.1085, F.1090 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: I.1119, N.1121 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain B: Y.15, F.46, N.48 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain B: N.267, N.269 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain B: N.318, Q.567 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain B: N.330 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain B: N.590 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: H.642, N.644 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain B: N.696, G.1118 Chain C: D.783 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain B: A.693, E.1059, K.1060, N.1061 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain B: N.704, L.909, Q.913, Q.1058 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: N.788, S.790 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: N.1085, T.1087, F.1090 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.1121 Ligand excluded by PLIP NAG.27: 5 residues within 4Å: Chain C: N.109, T.111, V.114, K.116, E.141 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain B: E.452 Chain C: T.95, N.221, T.223 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain B: K.545 Chain C: N.267, E.268, N.269 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: N.330, S.358, S.360 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain C: N.590 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain C: N.603, C.604, T.605, Q.631 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: H.642, N.644 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain A: D.783 Chain C: N.696, I.1117, G.1118 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: N.704, Q.913 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain C: A.693, E.1059, K.1060, N.1061 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain C: S.99, E.119, N.151, N.152 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: N.788, S.790, Q.791 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: N.1085, T.1087, F.1090 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain C: N.1121 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, K. et al., Identification of nano-abzymes to catalyze the spike-trimer of SARS-CoV-2. To Be Published

Release Date

2023-09-13

Peptides

Spike glycoprotein: ABC
VHH21: DE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Spike glycoprotein

VHH21