SMTL ID : 7ldj.2 (3 other biounits)

SARS-CoV-2 receptor binding domain in complex with WNb-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.36 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAG-NAG-MAN-MAN-NAG-FUL.1: 8 residues within 4Å: Chain A: G.9, F.12, N.13, L.38, S.41, N.110, L.111 Ligands: MAN.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.110

1 x MAN: alpha-D-mannopyranose(Non-covalent)

MAN.2: 4 residues within 4Å: Chain A: N.40, S.41, A.42 Ligands: NAG-NAG-MAN-MAN-NAG-FUL.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.40, A:A.42

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pymm, P. et al., SARS-CoV-2 receptor binding domain in complex with WNb-2. Proc.Natl.Acad.Sci.USA (2021)

Release Date

2021-05-05

Peptides

Spike glycoprotein: A
Nanobody 2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
F

Spike glycoprotein

Nanobody 2

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