SMTL ID : 7oaq.1

Nanobody H3 AND C1 bound to RBD with Kent mutation

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 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.9, G.10, F.13, N.14 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.9, B:F.13 Water bridges: B:N.14

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

CIT.2: 7 residues within 4Å: Chain B: R.74, D.76, E.77, Q.80, G.87, K.88, I.89 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:K.88 Hydrogen bonds: B:R.74, B:E.77, B:Q.80, B:K.88, B:I.89 Water bridges: B:D.76, B:R.79, B:Y.176, B:Y.176, B:Y.176 Salt bridges: B:R.74

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

H3: A
Spike protein S1: B
H3: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
EEE

C
FFF

H3

Spike protein S1

H3

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