SMTL ID : 7ukl.1

Cryo-EM structure of Antibody 12-16 in complex with prefusion SARS-CoV-2 Spike glycoprotein

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

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

NAG.1: 2 residues within 4Å: Chain B: H.655, N.657 Ligand excluded by PLIP NAG.2: 3 residues within 4Å: Chain B: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.3: 3 residues within 4Å: Chain B: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.4: 3 residues within 4Å: Chain B: N.280, E.281, N.282 Ligand excluded by PLIP NAG.5: 2 residues within 4Å: Chain B: I.1132, N.1134 Ligand excluded by PLIP NAG.6: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.7: 4 residues within 4Å: Chain B: N.717, L.922, Q.926, Q.1071 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain B: N.801, S.803 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain B: Y.28, F.59, N.61 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain B: T.108, N.234, T.236 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain B: E.132, N.164, N.165 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain B: N.603, T.604 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain B: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain B: F.338, G.339, F.342, N.343 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain B: N.331, Q.580 Chain C: S.75 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain B: N.122, T.124 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain E: N.616, T.618 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain E: H.655, N.657 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain E: N.709, G.1131 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain E: N.280, E.281, N.282 Ligand excluded by PLIP NAG.21: 5 residues within 4Å: Chain E: N.331, K.529, Q.580 Chain G: S.75, K.76 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain E: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain E: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain E: N.717, L.922, Q.926, Q.1071 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain E: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain E: I.1132, N.1134 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain E: N.122, T.124, N.125, V.171 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain E: Y.28, N.61 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain B: E.465 Chain E: T.108, N.234, T.236 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain E: N.164, N.165 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain E: N.603 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain E: G.339, F.342, N.343, S.373 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain F: N.603 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain F: N.616, T.618 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain F: N.657 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain B: D.796 Chain F: N.709, G.1131 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain F: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain F: N.331 Chain H: N.77 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain F: N.280, E.281, N.282 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain F: I.1132, N.1134 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain F: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain F: N.717, L.922, Q.926, Q.1071 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain F: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain F: N.122, T.124, N.125, V.127 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain F: Y.28, N.61 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain F: T.108, N.234, T.236 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain F: N.164, N.165 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain F: F.338, G.339, F.342, 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

12-16 Fab Light Chain: ADI
Spike glycoprotein: BEF
12-16 Fab Heavy Chain: CGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
Y

D
L

I
N

B
B

E
C

F
A

C
X

G
H

H
M

12-16 Fab Light Chain

Spike glycoprotein

12-16 Fab Heavy Chain

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