SMTL ID : 8rj7.1 (4 other biounits)

The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the neutralizing nanobody 1.29

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: F.9, G.10, F.13, N.14 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.9, A:F.13

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 2 residues within 4Å: Chain A: G.87, K.88 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.88 Water bridges: A:E.77, A:E.77, A:E.77, A:I.89 Salt bridges: A:K.88 SO4.3: 3 residues within 4Å: Chain B: S.7, R.19, S.21 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.7, B:S.21, B:S.21 Water bridges: B:R.19, B:R.19 Salt bridges: B:R.19

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Casasnovas, J.M. et al., The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the neutralizing nanobody 1.29. To Be Published

Release Date

2024-11-27

Peptides

Spike protein S1: A
Camel-derived nanobody 1.29: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Spike protein S1

Camel-derived nanobody 1.29

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