SMTL ID : 8cwi.1

Fab arm of antibody 10G4 bound to CoV-2 receptor binding domain (RBD)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG-NAG-BMA-MAN-MAN-FUC.1: 7 residues within 4Å: Chain A: F.6, G.7, F.10, N.11, V.35, N.38, S.39 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.39

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.2: 3 residues within 4Å: Chain C: S.12, S.14, N.107 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-functional Binders)

MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 4 residues within 4Å: Chain B: E.46, W.47 Chain C: T.97, F.98 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain B: K.121, G.122 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain C: N.1, I.2, Q.3, R.26, Q.27 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Langley, D.B. et al., Neutralization of CoV-2 omicron lineages by affinity-matured class 5 antibodies. To Be Published

Release Date

2023-05-24

Peptides

Spike protein S1: A
Heavy chain of Fab arm of antibody 10G4: B
Light chain of Fab arm of antibody 10G4: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

Spike protein S1

Heavy chain of Fab arm of antibody 10G4

Light chain of Fab arm of antibody 10G4

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