SMTL ID : 7neg.1

Crystal structure of the N501Y mutant receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-269 Fab

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG-NAG-FUC.1: 3 residues within 4Å: Chain C: F.20, G.21, N.25 No protein-ligand interaction detected (PLIP)

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 12 residues within 4Å: Chain A: F.170, P.171, A.172, V.173, S.181, L.182, S.183 Chain B: Q.161, E.162, S.163, S.177, T.179 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:Q.161, B:T.179, B:T.179, A:F.170, A:V.173, A:S.183 Water bridges: B:T.179, A:S.181 GOL.4: 6 residues within 4Å: Chain A: F.99, D.105 Chain B: Q.55, S.56 Chain C: G.167, F.168 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: B:Q.55, B:Q.55, C:G.167, A:D.105 GOL.5: 7 residues within 4Å: Chain A: V.167, H.168, T.169 Chain B: T.165, E.166, Q.167, D.168 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.167, B:D.168, A:H.168, A:T.169 GOL.6: 3 residues within 4Å: Chain B: S.93, Y.94, A.96 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.93 GOL.8: 3 residues within 4Å: Chain A: F.99, Y.100 Chain C: Q.175 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Q.175, A:Y.100

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 3 residues within 4Å: Chain A: N.30, R.71, N.73 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:N.30, A:N.73 Salt bridges: A:R.71, C:K.140 SO4.7: 1 residues within 4Å: Chain B: R.212 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.212 SO4.9: 5 residues within 4Å: Chain A: S.25, G.26, L.27, N.76 Chain C: S.159 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:G.26, A:N.76, C:S.159, C:S.159

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Supasa, P. et al., Reduced neutralization of SARS-CoV-2 B.1.1.7 variant by convalescent and vaccine sera. Cell (2021)

Release Date

2021-03-03

Peptides

Antibody COVOX-269 Fab heavy chain: A
Antibody COVOX-269 Fab light chain: B
Surface glycoprotein: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
E

Antibody COVOX-269 Fab heavy chain

Antibody COVOX-269 Fab light chain

Surface glycoprotein

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