SMTL ID : 7p19.1 (1 other biounit)

Crystal structure of SARS-CoV-2 RBD Q498Y complexed with human ACE2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.24 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: K.10, N.74 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.10 NAG.3: 2 residues within 4Å: Chain A: S.404, N.530 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.404, A:S.404 NAG.5: 1 residues within 4Å: Chain B: N.12 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.358, E.359, H.362, E.386 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.358, A:H.362, A:E.386

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

EDO.4: 3 residues within 4Å: Chain A: R.257, H.489, Y.499 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.257, A:R.257, A:H.489, A:R.502, A:R.502

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

CL.6: 6 residues within 4Å: Chain B: S.18, V.19, V.70, Y.120, L.121, Y.164 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Erausquin, E. et al., Structural bases for the higher adherence to ACE2 conferred by the SARS-CoV-2 spike Q498Y substitution. Acta Crystallogr D Struct Biol (2022)

Release Date

2022-07-13

Peptides

Processed angiotensin-converting enzyme 2: A
Spike protein S1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

Processed angiotensin-converting enzyme 2

Spike protein S1

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