SMTL ID : 7xmz.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.2: 2 residues within 4Å: Chain A: N.280, N.282 Ligand excluded by PLIP NAG.3: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.4: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.6: 2 residues within 4Å: Chain A: N.709, G.1131 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: A.706, N.1074 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain A: Y.28, F.59, N.61 Ligand excluded by PLIP NAG.9: 4 residues within 4Å: Chain A: G.232, I.233, N.234 Chain B: H.519 Ligand excluded by PLIP NAG.10: 4 residues within 4Å: Chain A: Q.115, E.132, N.165 Chain H: A.75 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain B: N.280, E.281, N.282 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain B: H.655, N.657 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain B: N.616 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain B: N.709, G.1131 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: A.706, N.1074 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: F.59, N.61 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain B: G.232, I.233, N.234 Chain C: H.519 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: E.132, N.165 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain C: H.655, N.657 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain C: N.616, T.618 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: D.796 Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain C: A.706, N.1074 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain C: Y.28, F.59, N.61 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: G.232, I.233, N.234 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain C: N.165 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
D2 heavy chain: DFH
D2 light chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

F
D

H
G

E
L

G
E

I
I

Spike glycoprotein

D2 heavy chain

D2 light chain

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