SMTL ID : 7spp.1

Crystal structure of the SARS-CoV-2 receptor binding domain in complex with VNAR 2C02

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

hetero-1-1-mer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: R.37, Y.78, F.146, S.196, E.198 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.37, A:R.37, A:E.198 EDO.3: 3 residues within 4Å: Chain A: P.203, A.204, C.207 No protein-ligand interaction detected (PLIP)

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 5 residues within 4Å: Chain A: G.21, F.24, N.25, V.49, L.50 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.24 Hydrogen bonds: A:N.25

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

CL.4: 5 residues within 4Å: Chain B: V.57, E.58, S.59, S.68, R.70 Ligand excluded by PLIP

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 2C02: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Spike protein S1

VNAR 2C02

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