SMTL ID : 7nxa.1

Crystal structure of the receptor binding domain of SARS-CoV-2 B.1.351 variant Spike glycoprotein in complex with COVOX-222 and EY6A Fabs

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

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

Ligands

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

SO4.1: 1 residues within 4Å: Chain B: R.18 Ligand excluded by PLIP SO4.2: 3 residues within 4Å: Chain B: S.52, S.53, L.54 Ligand excluded by PLIP SO4.3: 2 residues within 4Å: Chain B: R.18, T.20 Ligand excluded by PLIP SO4.4: 4 residues within 4Å: Chain B: S.60, R.61, S.76 Ligands: SO4.5 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain B: S.76, S.77 Ligands: SO4.4 Ligand excluded by PLIP SO4.10: 5 residues within 4Å: Chain C: S.154 Chain D: S.25, G.26, L.27, N.76 Ligand excluded by PLIP SO4.11: 5 residues within 4Å: Chain C: R.134, S.136, N.137, K.139, E.142 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain C: R.34, N.37, N.71 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain C: I.145, S.146, T.147 Ligand excluded by PLIP SO4.15: 1 residues within 4Å: Chain D: K.75 Ligand excluded by PLIP SO4.16: 9 residues within 4Å: Chain D: P.173, V.175, S.183, L.184, S.185 Chain E: Q.160, S.162, S.176, T.178 Ligand excluded by PLIP SO4.17: 7 residues within 4Å: Chain C: N.94, L.132 Chain D: Y.33, Y.52, E.99, S.101 Chain E: Y.92 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain D: D.72, N.73, S.74 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain C: Y.166 Chain D: G.103, W.105 Ligand excluded by PLIP SO4.20: 4 residues within 4Å: Chain D: T.113, L.114, P.155, K.207 Ligand excluded by PLIP SO4.21: 1 residues within 4Å: Chain E: R.211 Ligand excluded by PLIP SO4.22: 2 residues within 4Å: Chain E: G.9, T.10 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain E: S.121, D.122, E.123 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain E: K.40, Q.43, R.46 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain C: T.53, G.81, V.84, V.180, Y.185 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.53, C:T.53, C:V.180 Water bridges: C:R.85 GOL.14: 5 residues within 4Å: Chain D: Q.177, S.178 Chain E: G.157, N.158, Q.160 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:S.178, E:N.158

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

NAG.7: 6 residues within 4Å: Chain C: F.15, G.16, F.19, N.20, L.45, S.48 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.19, C:L.45 Hydrogen bonds: C:N.20

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 5 residues within 4Å: Chain C: F.24, S.26, Y.28, N.127, Y.128 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.26, C:S.26, C:Y.28, C:Y.28 PEG.9: 5 residues within 4Å: Chain C: Q.175, Y.178 Chain E: P.30, S.31, S.32 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain C Hydrogen bonds: E:S.31, E:S.32, E:S.32, C:Q.175, C:Y.178

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dejnirattisai, W. et al., Antibody evasion by the P.1 strain of SARS-CoV-2. Cell (2021)

Release Date

2021-04-07

Peptides

EY6A Fab heavy chain: A
EY6A Fab light chain: B
Spike protein S1: C
COVOX-222 Fab heavy chain: D
COVOX-222 Fab light chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
E

D
A

E
B

EY6A Fab heavy chain

EY6A Fab light chain

Spike protein S1

COVOX-222 Fab heavy chain

COVOX-222 Fab light chain

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