SMTL ID : 7ufl.2 (1 other biounit)

Crystal structure of chimeric omicron RBD (strain BA.2) complexed with chimeric mouse ACE2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.84 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain A: N.35, T.37, E.39, N.40, R.322 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.39

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.2: 4 residues within 4Å: Chain A: S.402, D.525, S.527, N.528 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.356, E.357, H.360, E.384 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.356, A:H.360, A:E.384, H2O.1, H2O.1

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

CL.4: 3 residues within 4Å: Chain A: R.151, W.459, D.481 Ligand excluded by PLIP

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 10 residues within 4Å: Chain A: A.135, N.136, S.137, L.138, R.143, Y.234, N.259, L.260, S.262, L.263 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.234, A:S.262 EDO.6: 3 residues within 4Å: Chain A: G.301, Q.534, F.537 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.534 EDO.8: 3 residues within 4Å: Chain A: Y.261, N.272, D.274 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.272, A:D.274, A:D.274 EDO.9: 2 residues within 4Å: Chain A: A.330, H.360 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.330, A:A.330

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

NAG.7: 2 residues within 4Å: Chain A: F.267, N.414 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.267 NAG.10: 4 residues within 4Å: Chain B: F.20, G.21, F.24, N.25 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.20, B:F.24

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, W. et al., Structural basis for mouse receptor recognition by SARS-CoV-2 omicron variant. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-10-19

Peptides

Angiotensin-converting enzyme 2: A
Spike protein S1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
F

Angiotensin-converting enzyme 2

Spike protein S1

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