SMTL ID : 7sn0.1 (1 other biounit)

Crystal structure of spike protein receptor binding domain of escape mutant SARS-CoV-2 from immunocompromised patient (d146*) in complex with human receptor ACE2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.08 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN.1: 8 residues within 4Å: Chain A: A.71, K.74, E.75, S.77, T.78, Q.81, N.103, S.106 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.74 Hydrogen bonds: A:E.75

2 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: 5 residues within 4Å: Chain A: K.309, E.312, K.313, V.316, N.322 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 4 residues within 4Å: Chain A: S.420, D.543, S.545, N.546 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.420

1 x NAG- NAG- BMA- MAN- NAG- GAL- NAG- MAN- NAG- GAL: beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)]alpha-D-mannopyranose-(1-3)-[beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-mannopyranose-(1-6)]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-NAG-GAL-NAG-MAN-NAG-GAL.4: 6 residues within 4Å: Chain A: N.53, T.55, E.57, N.58, Q.340 Chain B: K.174 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.174

1 x NAG- NAG- BMA- MAN- NAG- GAL- NAG- GAL- MAN- NAG: beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]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-NAG-GAL-NAG-GAL-MAN-NAG.5: 11 residues within 4Å: Chain A: K.26, H.34, N.90, T.92, V.93, A.387, P.389 Chain B: R.133, R.138, Q.144, T.145 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.135, B:R.138, B:R.138

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.6: 3 residues within 4Å: Chain B: N.73, V.97, S.101 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 4 residues within 4Å: Chain A: H.374, E.375, H.378, E.402 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.374, A:H.378, A:E.402, A:E.402

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

CL.8: 4 residues within 4Å: Chain A: R.169, W.477, W.478, D.499 Ligand excluded by PLIP

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

NAG.9: 2 residues within 4Å: Chain A: N.432, E.433 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.433, A:E.433

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nabel, K.G. et al., Structural basis for continued antibody evasion by the SARS-CoV-2 receptor binding domain. Science (2022)

Release Date

2021-12-08

Peptides

Angiotensin-converting enzyme 2: A
Surface glycoprotein: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Angiotensin-converting enzyme 2

Surface glycoprotein

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