SMTL ID : 7e9o.1

Cryo-EM structure of the SARS-CoV-2 S-6P in complex with 35B5 Fab(3 up RBDs, state2)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: E.281, N.282 Ligand excluded by PLIP NAG.2: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.3: 2 residues within 4Å: Chain A: N.709, G.1131 Ligand excluded by PLIP NAG.4: 1 residues within 4Å: Chain A: N.717 Ligand excluded by PLIP NAG.5: 2 residues within 4Å: Chain A: N.801, S.803 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain A: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.7: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.8: 5 residues within 4Å: Chain A: N.1098, G.1099, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain B: E.281, N.282 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.12: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain B: N.616 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain B: N.709 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain B: N.717 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain B: N.801, S.803 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain B: N.1134 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: E.1072, N.1074 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain C: I.1132, N.1134 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: K.558 Chain C: E.281, N.282 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain C: N.331, Q.580 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain C: N.616, T.618 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: D.796 Chain C: N.709 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain C: N.717, Q.926 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain C: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain C: N.1098, H.1101, F.1103 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, X. et al., A potent human monoclonal antibody with pan-neutralizing activities directly dislocates S trimer of SARS-CoV-2 through binding both up and down forms of RBD. Signal Transduct Target Ther (2022)

Release Date

2022-03-09

Peptides

Spike glycoprotein: ABC
Light chain of 35B5 Fab: DFH
Heavy chain of 35B5 Fab: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
C

D
L

F
O

H
X

E
H

G
P

I
Y

Spike glycoprotein

Light chain of 35B5 Fab

Heavy chain of 35B5 Fab

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