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

Crystal structure of the T478K mutant receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-45 and COVOX-253 Fabs

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-1-1-1-1-1-mer

Ligands

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 4 residues within 4Å: Chain A: G.16, F.19, N.20, L.45 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.19, A:L.45

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.2: 5 residues within 4Å: Chain D: H.100, N.102, S.105, C.106, Y.107 No protein-ligand interaction detected (PLIP)

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: N.20, S.50, W.113 No protein-ligand interaction detected (PLIP) GOL.4: 6 residues within 4Å: Chain A: E.142, R.143 Chain B: Y.59, Y.105, Y.106 Chain C: N.93 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Water bridges: B:Y.105 Hydrogen bonds: C:N.93 GOL.8: 3 residues within 4Å: Chain D: V.93, Q.115, G.116 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.116

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

CL.5: 3 residues within 4Å: Chain B: R.72, D.73, N.74 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain B: N.57, K.58 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain C: Q.37 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain D: R.44, E.46, W.47 Chain E: T.98, F.99 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain D: V.173, H.174 Chain E: D.168 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, C. et al., Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum. Cell (2021)

Release Date

2021-07-07

Peptides

Spike protein S1: A
COVOX-45 Fab heavy chain: B
COVOX-45 Fab light chain: C
COVOX-253 Fab heavy chain: D
COVOX-253 Fab light chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
R

B
A

C
B

D
F

E
G

Spike protein S1

COVOX-45 Fab heavy chain

COVOX-45 Fab light chain

COVOX-253 Fab heavy chain

COVOX-253 Fab light chain

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