SMTL ID : 8g7b.1

SARS-CoV-2 spike/Nb3 complex with 1 RBD up and 2 Nb3 (local refinement)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-3-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain B: N.318, P.566, Q.567 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.318, B:P.566 NAG.2: 5 residues within 4Å: Chain B: F.325, G.326, F.329, N.330, V.354 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.329 Hydrogen bonds: B:N.330 NAG.3: 3 residues within 4Å: Chain C: N.318, Q.567, L.569 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.569 Hydrogen bonds: C:Q.567 NAG.4: 2 residues within 4Å: Chain C: N.330, V.354 No protein-ligand interaction detected (PLIP) NAG.5: 6 residues within 4Å: Chain A: S.27, G.28 Chain C: S.99, E.119, N.151, N.152 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:E.119, C:E.119, A:S.27 NAG.6: 2 residues within 4Å: Chain E: N.318, Q.567 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.318, E:Q.567 NAG.7: 4 residues within 4Å: Chain E: F.325, G.326, F.329, N.330 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:F.329 Hydrogen bonds: E:N.330

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ye, G. et al., SARS-CoV-2 spike/Nb3 complex with 1 RBD up and 2 Nb3. To Be Published

Release Date

2024-02-21

Peptides

Nanosota-3: AD
Spike glycoprotein: BCE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

D
C

B
A

C
B

E
D

Nanosota-3

Spike glycoprotein

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