SMTL ID : 8vqr.1 (1 other biounit)

Crystal structure of chimeric SARS-CoV-2 RBD complexed with chimeric raccoon dog ACE2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.57 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 7 residues within 4Å: Chain A: T.33, N.34, T.36, N.39, M.313, P.317, W.321 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.321, A:P.317 Hydrogen bonds: A:N.39, A:N.39, A:T.33

1 x NAG- NAG- BMA- BMA- FUC: beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-BMA-FUC.2: 14 residues within 4Å: Chain A: L.54, N.84, Y.183, T.328, A.329, E.356, H.359, D.363, F.371, L.372, R.374, N.375, E.383 Ligands: ZN.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.371, A:A.329, A:E.356, A:D.363, A:E.383, A:E.383

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.3: 2 residues within 4Å: Chain A: S.401, N.527 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.401

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.4: 5 residues within 4Å: Chain B: F.20, G.21, F.24, N.25, V.49 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.5: 5 residues within 4Å: Chain A: H.355, E.356, H.359, E.383 Ligands: NAG-NAG-BMA-BMA-FUC.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.355, A:H.359, H2O.1

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

CL.6: 4 residues within 4Å: Chain A: R.150, W.458, W.459, D.480 Ligand excluded by PLIP

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

NAG.7: 1 residues within 4Å: Chain A: N.303 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hsueh, F. et al., Structural basis for raccoon dog receptor recognition by SARS-CoV-2. To Be Published

Release Date

2024-05-01

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

Angiotensin-converting enzyme,Processed angiotensin-converting enzyme 2

Spike protein S1

Related Entries With Identical Sequence