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

Crystal structure of the SARS-CoV-2 receptor binding domain in complex with VNAR 3B4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

hetero-1-1-mer

Ligands

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.1: 6 residues within 4Å: Chain A: F.12, G.13, F.16, N.17, L.42 Ligands: EDO.3 No protein-ligand interaction detected (PLIP)

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 8 residues within 4Å: Chain A: P.100, F.103, T.104, F.138, S.188, F.189, E.190, L.191 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.104 EDO.3: 6 residues within 4Å: Chain A: F.16, N.17, S.47, F.48, W.110 Ligands: NAG-NAG-FUC.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.16 EDO.4: 6 residues within 4Å: Chain A: R.20, F.21, A.22, S.23, N.124, Y.125 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.20, A:R.20, A:S.23 Water bridges: A:S.23, A:S.23, A:Y.125

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ubah, O.C. et al., Mechanisms of SARS-CoV-2 neutralization by shark variable new antigen receptors elucidated through X-ray crystallography. Nat Commun (2021)

Release Date

2022-01-05

Peptides

Spike protein S1: A
VNAR 3B4: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Spike protein S1

VNAR 3B4

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