SMTL ID : 7x93.1

The SARS-CoV-2 receptor binding domain bound with the Fab fragment of a human neutralizing antibody Ab765

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 7 residues within 4Å: Chain A: F.338, G.339, F.342, N.343, L.368, S.371, F.374 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.2: 9 residues within 4Å: Chain B: F.338, G.339, F.342, N.343, V.367 Chain E: F.456, F.486, N.487, Y.489 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Y.489, E:Y.489

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

NAG.3: 6 residues within 4Å: Chain E: F.338, G.339, F.342, N.343, L.368, F.374 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:F.342

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Takeshita, M. et al., Potent neutralizing broad-spectrum antibody against SARS-CoV-2 generated from dual-antigen-specific B cells from convalescents. Iscience (2023)

Release Date

2023-03-22

Peptides

Spike glycoprotein: ABE
Ab765 heavy chain: C
Ab765 light chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

E
G

C
E

D
F

Spike glycoprotein

Ab765 heavy chain

Ab765 light chain

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