SMTL ID : 8vqr.2 (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- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.1: 3 residues within 4Å: Chain A: S.401, D.524, N.527 No protein-ligand interaction detected (PLIP)

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.2: 3 residues within 4Å: Chain A: T.33, N.34, W.321 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- FUC: alpha-D-mannopyranose-(1-3)-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-MAN-FUC.3: 15 residues within 4Å: Chain A: W.50, L.54, N.84, Y.183, P.327, T.328, A.329, W.330, E.356, H.359, F.371, L.372, R.374, N.375, H.382 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.327, A:A.329, A:H.359, A:L.372 Hydrophobic interactions: A:F.371

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: H.355, E.356, H.359, E.383 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.355, A:H.359, A:E.383

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

CL.5: 4 residues within 4Å: Chain A: R.150, W.458, W.459, D.480 Ligand excluded by PLIP

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

EDO.6: 3 residues within 4Å: Chain A: G.300, Q.533, F.536 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.533 EDO.7: 8 residues within 4Å: Chain A: A.134, L.137, R.142, Y.233, N.258, L.259, S.261, L.262 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.233, A:S.261

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

NAG.8: 1 residues within 4Å: Chain A: N.413 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
B

B
F

Angiotensin-converting enzyme,Processed angiotensin-converting enzyme 2

Spike protein S1

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