SMTL ID : 7cm4.1

Crystal Structure of COVID-19 virus spike receptor-binding domain complexed with a neutralizing antibody CT-P59

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.71 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG- MAN- MAN- FUC: alpha-D-mannopyranose-(1-6)-alpha-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-MAN-MAN-FUC.1: 2 residues within 4Å: Chain A: G.21, N.25 No protein-ligand interaction detected (PLIP)

2 x NI: NICKEL (II) ION(Non-covalent)

NI.2: 4 residues within 4Å: Chain B: K.59, H.61, T.70, I.71 No protein-ligand interaction detected (PLIP) NI.5: 1 residues within 4Å: Chain C: H.192 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.192

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

EDO.3: 5 residues within 4Å: Chain C: N.31, N.32, Y.33, N.52, K.67 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.31, C:N.52, C:K.67 EDO.4: 4 residues within 4Å: Chain B: G.44 Chain C: D.86, E.106, K.167 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, C. et al., A therapeutic neutralizing antibody targeting receptor binding domain of SARS-CoV-2 spike protein. Nat Commun (2021)

Release Date

2021-01-20

Peptides

Spike glycoprotein: A
IgG heavy chain: B
IgG light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

Spike glycoprotein

IgG heavy chain

IgG light chain