SMTL ID : 7xo9.1

SARS-CoV-2 Omicron BA.2 Variant RBD complexed with human ACE2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 4 residues within 4Å: Chain B: R.169, W.477, K.481, D.499 Ligand excluded by PLIP

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 3 residues within 4Å: Chain B: H.374, H.378, E.402 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.374, B:E.402

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

NAG.3: 3 residues within 4Å: Chain B: S.420, S.545, N.546 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.420, B:S.420, B:S.420, B:S.545, B:N.546 NAG.4: 2 residues within 4Å: Chain B: N.322, M.323 No protein-ligand interaction detected (PLIP) NAG.5: 3 residues within 4Å: Chain B: K.26, Q.89, N.90 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.26, B:Q.89

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, Y. et al., Structural and biochemical mechanism for increased infectivity and immune evasion of Omicron BA.2 variant compared to BA.1 and their possible mouse origins. Cell Res. (2022)

Release Date

2022-06-15

Peptides

Spike glycoprotein: A
Angiotensin-converting enzyme 2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Spike glycoprotein

Angiotensin-converting enzyme 2

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