SMTL ID : 7e9n.1

Cryo-EM structure of the SARS-CoV-2 S-6P in complex with 35B5 Fab(1 down RBD, state1)

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.255, N.256 Ligand excluded by PLIP NAG.2: 2 residues within 4Å: Chain A: N.590, T.592 Ligand excluded by PLIP NAG.3: 3 residues within 4Å: Chain A: N.683, G.1105 Chain B: D.770 Ligand excluded by PLIP NAG.4: 1 residues within 4Å: Chain A: N.691 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain A: N.775, S.777, Q.778 Ligand excluded by PLIP NAG.6: 2 residues within 4Å: Chain A: A.680, N.1048 Ligand excluded by PLIP NAG.7: 1 residues within 4Å: Chain A: N.1108 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain A: N.1072, T.1074, H.1075 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: N.305, Q.554 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain B: N.256 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain B: A.680, E.1046, N.1048 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain B: N.305 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain B: N.590 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain B: N.683, G.1105 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain B: N.691 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain B: N.775, S.777, Q.778 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: I.1106, N.1108 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain B: N.1072, G.1073, H.1075, F.1077 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain C: E.255, N.256 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain C: N.305 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain C: N.590 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: D.770 Chain C: N.683, G.1105 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain C: N.691 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain C: N.775, S.777, Q.778 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain C: A.680, N.1048 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain C: N.1072, H.1075, F.1077 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain C: I.1106, N.1108 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

2022-04-06

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
O

F
X

H
L

E
P

G
Y

I
H

Spike glycoprotein

Light chain of 35B5 Fab

Heavy chain of 35B5 Fab

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