SMTL ID : 8g7c.1

local refinement of SARS-CoV-2 spike/Nb4 complex with 2 RBDs up and 3 Nb4 bound

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

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

NAG.1: 1 residues within 4Å: Chain A: N.221 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.221 NAG.2: 2 residues within 4Å: Chain A: E.268, N.269 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.268 NAG.3: 4 residues within 4Å: Chain A: P.317, N.318, P.566, Q.567 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.317 Hydrogen bonds: A:N.318 NAG.4: 2 residues within 4Å: Chain A: G.326, N.330 No protein-ligand interaction detected (PLIP) NAG.5: 2 residues within 4Å: Chain B: Y.15, N.48 No protein-ligand interaction detected (PLIP) NAG.6: 3 residues within 4Å: Chain A: E.452 Chain B: T.95, N.221 No protein-ligand interaction detected (PLIP) NAG.7: 3 residues within 4Å: Chain A: K.545 Chain B: E.268, N.269 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.545 Hydrogen bonds: A:K.545 NAG.8: 2 residues within 4Å: Chain B: N.318, Q.567 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.567 NAG.9: 2 residues within 4Å: Chain B: N.603, T.605 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.603, B:N.603 NAG.10: 1 residues within 4Å: Chain C: N.48 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:N.48 NAG.11: 2 residues within 4Å: Chain C: N.267, N.269 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.267 NAG.12: 2 residues within 4Å: Chain C: N.603, T.605 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.605, C:T.605

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ye, G. et al., local refinement of SARS-CoV-2 spike/Nb4 complex with 2 RBDs up and 3 Nb4 bound. To Be Published

Release Date

2024-02-21

Peptides

Spike glycoprotein: ABC
Nanosota-4: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
E

E
G

F
F

Spike glycoprotein

Nanosota-4

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