SMTL ID : 7olz.1

Crystal structure of the SARS-CoV-2 RBD with neutralizing-VHHs Re5D06 and Re9F06

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x DMX: 3-[BENZYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE(Non-covalent)

DMX.1: 8 residues within 4Å: Chain A: Y.34, R.74, D.75, N.76, K.78, N.79, T.80, V.81 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.74, A:V.81 Salt bridges: A:R.74

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

SO4.2: 3 residues within 4Å: Chain C: R.23, R.25, R.134 4 PLIP interactions: 4 interactions with chain C Water bridges: C:R.25, C:R.25 Salt bridges: C:R.25, C:R.134

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guttler, T. et al., Neutralization of SARS-CoV-2 by highly potent, hyperthermostable, and mutation-tolerant nanobodies. Embo J. (2021)

Release Date

2021-08-11

Peptides

Nanobody Re5D06: A
Nanobody Re9F06: B
Spike protein S1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
B

C
A

Nanobody Re5D06

Nanobody Re9F06

Spike protein S1

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