SMTL ID : 7spo.2 (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.2 No protein-ligand interaction detected (PLIP)

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

EDO.2: 6 residues within 4Å: Chain A: F.16, N.17, S.47, F.48, W.110 Ligands: NAG-NAG-FUC.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.17, A:S.47 EDO.3: 10 residues within 4Å: Chain A: P.100, D.102, F.103, T.104, F.138, S.188, F.189, E.190, L.191 Ligands: EDO.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.104, A:F.189 Water bridges: A:L.191 EDO.4: 6 residues within 4Å: Chain A: R.29, Y.70, F.138, S.188, E.190 Ligands: EDO.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.29, A:R.29 EDO.5: 3 residues within 4Å: Chain A: N.175, G.176, Y.179 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.175, A:G.176

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
B

B
D

Spike protein S1

VNAR 3B4

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