SMTL ID : 7ukm.1

Cryo-EM structure of Antibody 12-19 in complex with prefusion SARS-CoV-2 Spike glycoprotein

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: N.603, T.604, T.941 Ligand excluded by PLIP NAG.2: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.3: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.4: 3 residues within 4Å: Chain A: N.709, G.1131 Chain G: D.796 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain A: N.280, E.281, N.282 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain A: T.108, N.234, T.236 Ligand excluded by PLIP NAG.7: 3 residues within 4Å: Chain A: N.122, T.124, V.127 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain A: N.1098, T.1100, F.1103 Ligand excluded by PLIP NAG.9: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain A: N.717, Q.926, Q.1071 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: Y.28, N.30, N.61 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: E.132, N.164, N.165 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.331, T.333, Q.580 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: F.338, G.339, N.343 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: A.706, K.1073, N.1074 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain D: N.657 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain D: N.709, G.1131 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain D: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain D: N.280, E.281, N.282 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain D: T.108, N.234, T.236 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain D: N.331, S.530 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain D: N.1098, T.1100, F.1103 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain D: N.1134 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain D: N.717, Q.926, Q.1071 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain D: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain D: N.616, T.618 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain D: N.164, N.165 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain D: F.338, G.339, F.342, N.343 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain D: N.603 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain D: N.122, T.124 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain D: Y.28, N.61 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain G: N.603 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain G: N.616 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain G: N.657 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain G: N.709, G.1131 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain G: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain G: N.280, E.281, N.282 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain G: N.331, I.332 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain G: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain G: N.1134 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain G: N.717, Q.926, Q.1071 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain G: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain G: Y.28, N.61 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain G: E.132, N.164, N.165 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain G: T.108, N.234, T.236 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain G: F.338, G.339, N.343 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, L. et al., Antibodies targeting a quaternary site on SARS-CoV-2 spike glycoprotein prevent viral receptor engagement by conformational locking. Immunity (2023)

Release Date

2023-10-04

Peptides

Spike glycoprotein: ADG
12-19 Fab Heavy Chain: BEH
12-19 Fab Light Chain: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

D
A

G
C

B
X

E
H

H
M

C
Y

F
L

I
N

Spike glycoprotein

12-19 Fab Heavy Chain

12-19 Fab Light Chain

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