SMTL ID : 7oap.1

Nanobody H3 AND C1 bound to RBD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain B: F.8, G.9, F.12, N.13 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.8, B:F.12

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.2: 3 residues within 4Å: Chain B: W.23, R.25, R.136 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:W.23 Water bridges: B:R.25 Salt bridges: B:R.25, B:R.136

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

CL.3: 6 residues within 4Å: Chain C: S.35, R.54, W.55, I.103, V.104, Y.111 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huo, J. et al., A potent SARS-CoV-2 neutralising nanobody shows therapeutic efficacy in the Syrian golden hamster model of COVID-19. Nat Commun (2021)

Release Date

2021-08-11

Peptides

C1 nanobody: A
Spike protein S1: B
H3 nanobody: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
EEE

C
FFF

C1 nanobody

Spike protein S1

H3 nanobody

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