SMTL ID : 7xst.1

Cryo-EM structure of SARS-CoV-2 Omicron spike glycoprotein in complex with three F61 Fab and three D2 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-3-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: A.703, E.1069, N.1071 Ligand excluded by PLIP NAG.2: 3 residues within 4Å: Chain A: N.1095, G.1096, F.1100 Ligand excluded by PLIP NAG.3: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 Ligand excluded by PLIP NAG.4: 2 residues within 4Å: Chain A: N.706 Chain B: Y.793 Ligand excluded by PLIP NAG.5: 1 residues within 4Å: Chain A: N.654 Ligand excluded by PLIP NAG.6: 1 residues within 4Å: Chain A: N.613 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: T.304, N.600 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: N.160, T.162 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: G.229, I.230, N.231 Ligand excluded by PLIP NAG.10: 4 residues within 4Å: Chain A: N.277, E.278, N.279, T.281 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain B: E.1069, N.1071 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain B: N.1095, H.1098, F.1100 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain B: N.706 Chain C: Y.793 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain B: Y.652, N.654 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain B: N.613, Q.641 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: N.600, T.601 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: N.160, T.162 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain B: N.231 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain B: N.277, E.278, N.279, T.281 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain C: N.654 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain C: T.304, N.600 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain C: A.703, E.1069, N.1071 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain C: N.1131 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain C: N.613, Q.641 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain A: Y.793 Chain C: N.706 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain C: N.160, T.162 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: G.229, I.230, N.231 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain C: N.277, E.278, N.279, T.281 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, X. et al., Structural basis of a two-antibody cocktail exhibiting highly potent and broadly neutralizing activities against SARS-CoV-2 variants including diverse Omicron sublineages. Cell Discov (2022)

Release Date

2022-11-23

Peptides

Spike glycoprotein: ABC
F61 heavy chain: DHL
F61 light chain: EIM
D2 heavy chain: FJN
D2 light chain: GKO

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
L

H
H

L
D

E
M

I
I

M
E

F
N

J
J

N
F

G
O

K
K

O
G

Spike glycoprotein

F61 heavy chain

F61 light chain

D2 heavy chain

D2 light chain

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