SMTL ID : 7whh.1

Crystal structure of SARS-CoV-2 omicron RBD and human ACE2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- FUC- NAG: alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-FUC-NAG.1: 3 residues within 4Å: Chain A: K.9, N.73, T.75 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.357, E.358, H.361, E.385 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.357, A:H.361, A:E.385, A:E.385

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

CL.3: 4 residues within 4Å: Chain A: R.152, W.460, W.461, D.482 Ligand excluded by PLIP

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

NAG.4: 3 residues within 4Å: Chain A: S.403, D.526, N.529 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.403, A:S.403, A:S.403, A:N.529 NAG.5: 1 residues within 4Å: Chain A: N.305 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.305 NAG.6: 5 residues within 4Å: Chain A: N.36, T.38, E.40, N.41, Q.323 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.36, A:E.40, A:N.41 NAG.7: 2 residues within 4Å: Chain B: D.7, N.11 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lan, J. et al., Structural insights into the SARS-CoV-2 Omicron RBD-ACE2 interaction. Cell Res. (2022)

Release Date

2022-06-01

Peptides

Processed angiotensin-converting enzyme 2: A
Spike glycoprotein: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

Processed angiotensin-converting enzyme 2

Spike glycoprotein