SMTL ID : 8jam.1

Cryo-EM structure of Omicron BA.1 RBD in complex with W328-6H2 (local refinement)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-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: 14 residues within 4Å: Chain A: F.335, D.336, F.339, N.340, V.364, L.365, L.368, A.369, F.371 Chain B: Q.1, L.95 Chain C: S.61, G.62, V.63 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.61, C:S.61, C:G.62, C:G.62

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

NAG.2: 4 residues within 4Å: Chain A: Y.366, N.367, T.382 Ligands: NAG.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.366 Hydrogen bonds: A:Y.366, A:N.367 NAG.3: 6 residues within 4Å: Chain A: T.382, K.383, N.385, D.386, P.524 Ligands: NAG.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.386, A:P.524 Hydrogen bonds: A:N.385

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nan, X.Y. et al., Cryo-EM structure of Omicron BA.1 RBD in complex with W328-6H2 (local refinement). To Be Published

Release Date

2024-12-18

Peptides

Spike glycoprotein: A
H chain of W328-6H2: B
L chain of W328-6H2: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
H

C
L

Spike glycoprotein

H chain of W328-6H2

L chain of W328-6H2

Related Entries With Identical Sequence