SMTL ID : 7q3r.1

Crystal structure of SARS-CoV-2 RBD in complex with the neutralizing nanobodies VHH-F04 and VHH-G09

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain A: F.8, G.9, F.12, N.13, F.37 No protein-ligand interaction detected (PLIP)

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

CL.2: 4 residues within 4Å: Chain A: G.172, V.173, G.174, Y.175 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: V.52, S.53, L.60 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: R.127, K.128, S.129 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain B: Y.63, V.67, K.68, G.69 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain B: R.75, D.76, N.77 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fernandez, I. et al., NANOBODIES AGAINST SARS-COV-2 NEUTRALIZE VARIANTS OF CONCERN AND EXPLORE CONFORMATIONAL DIFFERENCES ON THE SPIKE PROTEIN. To Be Published

Release Date

2022-11-16

Peptides

Spike glycoprotein: A
VHH-F04: B
VHH-G09: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
F

C
G

Spike glycoprotein

VHH-F04

VHH-G09

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