SMTL ID : 8gz5.1

Crystal structure of neutralizing VHH P17 in complex with SARS-CoV-2 Alpha variant spike receptor-binding domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.1: 6 residues within 4Å: Chain A: F.6, G.7, F.10, N.11, V.35, L.36 No protein-ligand interaction detected (PLIP)

12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 5 residues within 4Å: Chain A: F.10, N.11, S.41, F.42, W.104 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.10 EDO.3: 6 residues within 4Å: Chain A: F.15, A.16, S.17, N.118, Y.119 Ligands: EDO.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.17 Water bridges: A:N.118 EDO.4: 8 residues within 4Å: Chain A: T.44, K.46, Y.48, V.75, R.76, I.78, A.79, V.101 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.46, A:Y.48 Water bridges: A:R.76 EDO.5: 8 residues within 4Å: Chain A: D.96, F.97, T.98, F.132, S.182, F.183, E.184 Ligands: EDO.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.98, A:F.183 Water bridges: A:T.98, A:E.184 EDO.6: 5 residues within 4Å: Chain A: C.148, V.151, G.153, C.156 Chain B: N.54 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.151 EDO.7: 5 residues within 4Å: Chain A: R.71, Y.163, F.165, Y.169, Y.173 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.71, A:Y.173 Water bridges: A:Y.121 EDO.8: 5 residues within 4Å: Chain A: R.23, Y.64, F.132, E.184 Ligands: EDO.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.23, A:R.23, A:E.184 Water bridges: A:E.184 EDO.9: 3 residues within 4Å: Chain A: S.43, T.44, F.45 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.45 EDO.10: 4 residues within 4Å: Chain A: R.14, F.15, A.16 Ligands: EDO.3 No protein-ligand interaction detected (PLIP) EDO.11: 3 residues within 4Å: Chain A: W.21, R.23, F.132 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.132 Water bridges: A:R.134 EDO.12: 4 residues within 4Å: Chain A: G.153, F.154 Chain B: T.52, W.101 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.153 Water bridges: A:F.154, A:N.155, A:N.155 EDO.13: 2 residues within 4Å: Chain A: V.151 Chain B: N.54 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.53

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yamaguchi, K. et al., Structural insights into the rational design of a nanobody that binds with high affinity to the SARS-CoV-2 spike variant. J.Biochem. (2023)

Release Date

2022-12-07

Peptides

Spike protein S1: A
Nanobody P17: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Spike protein S1

Nanobody P17

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