SMTL ID : 8owt.1

SARS-CoV-2 spike RBD with A8 and H3 nanobodies bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.37 Å

Oligo State

hetero-2-2-2-mer

Ligands

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

NAG.1: 6 residues within 4Å: Chain B: F.9, G.10, F.13, N.14, V.38, L.39 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.13, B:L.39 Water bridges: B:V.38 NAG.2: 5 residues within 4Å: Chain E: F.9, G.10, F.13, N.14, L.39 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:F.9, E:F.13, E:L.39

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.3: 4 residues within 4Å: Chain B: N.2 Chain E: W.24, R.26, F.135 2 PLIP interactions: 2 interactions with chain E Water bridges: E:R.137 Salt bridges: E:R.26

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cornish, K.A.S. et al., Trimeric nanobodies potently neutralize Omicron variants of SARS-CoV-2. To Be Published

Release Date

2024-05-08

Peptides

Nanobody A8: AD
Spike protein S1: BE
Nanobody H3: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

D
DDD

B
BBB

E
EEE

C
CCC

F
FFF

Nanobody A8

Spike protein S1

Nanobody H3

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