SMTL ID : 7z1c.2 (1 other biounit)

Nanobody H11-B5 and H11-F2 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: 5 residues within 4Å: Chain A: G.10, F.13, N.14, V.38, L.39 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.13, A:V.38, A:L.39 Water bridges: A:G.10, A:N.14

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 5 residues within 4Å: Chain A: G.75, D.76, V.174, G.175, Y.179 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.76, A:D.76 PEG.3: 5 residues within 4Å: Chain A: F.13, N.14, S.44, F.45, W.107 No protein-ligand interaction detected (PLIP) PEG.4: 3 residues within 4Å: Chain A: S.46 Chain B: R.108, T.110 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.108, B:T.110, B:T.110

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mikolajek, H. et al., Correlation between the binding affinity and the conformational entropy of nanobody SARS-CoV-2 spike protein complexes. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-03-23

Peptides

Spike protein S1: A
Nanobody F2: B
Nanobody B5: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
E

Spike protein S1

Nanobody F2

Nanobody B5

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