SMTL ID : 7msq.2 (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

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

CL.1: 1 residues within 4Å: Chain A: P.131 Ligand excluded by PLIP CL.3: 4 residues within 4Å: Chain B: W.47, Y.59 Chain C: Y.94, P.95 Ligand excluded by PLIP CL.4: 1 residues within 4Å: Chain B: G.120 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain C: S.114, N.137 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain C: A.50, L.91 Ligand excluded by PLIP

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

SCN.2: 3 residues within 4Å: Chain A: A.20, R.134, I.136 No protein-ligand interaction detected (PLIP) SCN.8: 6 residues within 4Å: Chain C: T.197, H.198, L.201, S.202, S.203, P.204 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain B: Y.159, E.162, P.163, V.164, F.180, P.181, A.182, L.192 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.159, B:E.162, B:V.164, B:V.164, B:A.182

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
B

B
D

C
E

Spike protein S1

AB-3467 Fab Heavy Chain

AB-3467 Fab Light Chain

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