SMTL ID : 7msq.1 (1 other biounit)

Complex between the Fab arm of AB-3467 and the SARS-CoV-2 receptor binding domain (RBD)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- FUC: alpha-D-mannopyranose-(1-3)-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-FUC.1: 6 residues within 4Å: Chain A: F.6, G.7, F.10, N.11, L.36, S.39 No protein-ligand interaction detected (PLIP)

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

CL.2: 3 residues within 4Å: Chain A: R.125, K.126, S.127 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain B: Y.59 Chain C: Y.94 Ligand excluded by PLIP

3 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.4: 3 residues within 4Å: Chain C: Q.37, N.45, P.59 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.61 SCN.5: 4 residues within 4Å: Chain B: T.197 Chain C: S.114, N.137, N.138 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.114, C:N.138 Water bridges: C:S.114 SCN.6: 9 residues within 4Å: Chain B: H.178 Chain C: N.138, T.164, E.165, Q.166, D.167, T.172, Y.173, S.174 1 PLIP interactions: 1 interactions with chain B Water bridges: B:H.178

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Burnett, D.L. et al., Immunizations with diverse sarbecovirus receptor-binding domains elicit SARS-CoV-2 neutralizing antibodies against a conserved site of vulnerability. Immunity (2021)

Release Date

2022-01-19

Peptides

Spike protein S1: A
AB-3467 Fab Heavy Chain: B
AB-3467 Fab Light Chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

Spike protein S1

AB-3467 Fab Heavy Chain

AB-3467 Fab Light Chain

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