SMTL ID : 7c8v.1

Structure of sybody SR4 in complex with the SARS-CoV-2 S Receptor Binding domain (RBD)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-1-1-mer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: N.37, W.39, A.54, I.55, E.56, R.63 Chain B: Y.169 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:N.37, A:W.39, A:R.63, B:Y.127, B:Y.127 Water bridges: A:A.54, A:E.56, B:R.77 GOL.2: 4 residues within 4Å: Chain A: V.104, G.105 Chain B: E.158, F.164 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.158, B:E.158 GOL.3: 3 residues within 4Å: Chain B: R.20, F.21, N.28 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.28, B:N.28 GOL.5: 4 residues within 4Å: Chain B: G.78, R.82, V.177, Y.182 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.82, B:Y.182 Water bridges: B:T.50 GOL.6: 3 residues within 4Å: Chain B: P.86, G.87, D.101 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.86 GOL.7: 1 residues within 4Å: Chain B: R.140 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.140 GOL.8: 5 residues within 4Å: Chain B: R.82, Q.83, Q.88, T.89, G.90 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.83, B:Q.88, B:T.89 Water bridges: B:T.89, B:K.91 GOL.9: 2 residues within 4Å: Chain B: R.29, Y.70 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.29, B:Y.70

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

NAG.4: 4 residues within 4Å: Chain B: G.13, F.16, N.17, L.42 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.16, B:L.42

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, T. et al., A synthetic nanobody targeting RBD protects hamsters from SARS-CoV-2 infection. Nat Commun (2021)

Release Date

2020-06-24

Peptides

Synthetic nanobody SR4: A
Spike protein S1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Synthetic nanobody SR4

Spike protein S1

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