SMTL ID : 6vw1.2 (1 other biounit)

Structure of SARS-CoV-2 chimeric receptor-binding domain complexed with its receptor human ACE2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.68 Å

Oligo State

hetero-1-1-mer

Ligands

3 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: 2 residues within 4Å: Chain A: K.8, N.72 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 1 residues within 4Å: Chain A: N.304 No protein-ligand interaction detected (PLIP) NAG-NAG.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 NAG- NAG- BMA- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(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-NAG.2: 5 residues within 4Å: Chain A: S.402, P.408, D.525, S.527, N.528 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.408

1 x ZN: ZINC ION(Non-covalent)

ZN.5: 3 residues within 4Å: Chain A: P.328, E.357, E.384 No protein-ligand interaction detected (PLIP)

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

CL.6: 4 residues within 4Å: Chain A: R.151, W.459, K.463, D.481 Ligand excluded by PLIP

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

EDO.7: 9 residues within 4Å: Chain A: A.135, 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.8: 4 residues within 4Å: Chain A: G.301, L.302, Q.534, F.537 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.534 EDO.9: 4 residues within 4Å: Chain A: Y.225, K.229, P.266, Q.580 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.225, A:K.229, A:Q.580

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

NAG.10: 3 residues within 4Å: Chain A: F.267, N.414, E.415 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.267, A:E.415 Hydrogen bonds: A:N.414 NAG.11: 3 residues within 4Å: Chain A: Q.63, Q.83, N.85 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.63, A:N.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shang, J. et al., Structural basis of receptor recognition by SARS-CoV-2. Nature (2020)

Release Date

2020-03-04

Peptides

Angiotensin-converting enzyme 2: A
SARS-CoV-2 chimeric RBD: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
F

Angiotensin-converting enzyme 2

SARS-CoV-2 chimeric RBD

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