SMTL ID : 7nx6.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

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

Ligands

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

CL.1: 3 residues within 4Å: Chain A: Y.32, K.98, G.100 Ligand excluded by PLIP CL.2: 3 residues within 4Å: Chain A: T.28, F.29, S.30 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain C: Q.175, P.176, T.177 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain C: R.80, K.94, Y.130 Chain E: Y.92 Ligands: SO4.9 Ligand excluded by PLIP CL.12: 6 residues within 4Å: Chain D: Y.151, E.154, P.155, V.156, A.174, L.184 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain D: G.86, A.87 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain C: Q.175 Chain E: P.30, S.31, S.32 Ligand excluded by PLIP

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

SO4.3: 3 residues within 4Å: Chain B: K.39, K.42, K.45 4 PLIP interactions: 4 interactions with chain B Water bridges: B:K.45 Salt bridges: B:K.39, B:K.42, B:K.45 SO4.6: 4 residues within 4Å: Chain C: S.154 Chain D: S.25, G.26, L.27 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:S.154, D:G.26, D:L.27, D:N.76 SO4.7: 3 residues within 4Å: Chain C: R.134, K.139, E.142 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.142 Water bridges: C:R.134, C:K.139 Salt bridges: C:R.134, C:K.139 SO4.8: 2 residues within 4Å: Chain C: R.34, N.37 3 PLIP interactions: 3 interactions with chain C Water bridges: C:R.34, C:R.34 Salt bridges: C:R.34 SO4.9: 6 residues within 4Å: Chain C: Q.86, G.93, K.94 Chain D: Y.52 Chain E: Y.92 Ligands: CL.11 8 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D, 5 interactions with chain C Water bridges: E:Y.92, E:Y.92, C:K.94, C:K.94 Hydrogen bonds: D:Y.52, C:Q.86, C:K.94 Salt bridges: C:K.94 SO4.16: 1 residues within 4Å: Chain E: R.211 2 PLIP interactions: 2 interactions with chain E Water bridges: E:R.211 Salt bridges: E:R.211 SO4.17: 5 residues within 4Å: Chain E: K.40, R.46, P.60, R.62, E.82 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:E.82 Water bridges: E:K.40, E:D.83 Salt bridges: E:K.40, E:R.46, E:R.62 SO4.18: 4 residues within 4Å: Chain E: P.60, D.61, R.62, R.78 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:D.61 Salt bridges: E:R.62, E:R.78 SO4.19: 3 residues within 4Å: Chain E: P.8, G.9, T.10 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:G.9, E:T.10 SO4.20: 4 residues within 4Å: Chain E: T.10, K.103, D.105, R.142 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:D.105, E:R.142 Water bridges: E:K.103 Salt bridges: E:K.103

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain C: T.53, G.81, V.84, Y.185 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.52, C:T.53, C:T.53 GOL.14: 3 residues within 4Å: Chain D: D.107 Chain E: Y.50, T.57 8 PLIP interactions: 4 interactions with chain E, 1 interactions with chain C, 3 interactions with chain D Hydrogen bonds: E:Y.50, E:T.57, E:T.57, E:T.57, D:D.107, D:D.107 Water bridges: C:Y.166, D:W.105 GOL.15: 5 residues within 4Å: Chain D: T.166, G.168, V.169 Chain E: D.167, K.169 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:D.167 Water bridges: E:D.167

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

NAG.5: 3 residues within 4Å: Chain C: G.16, N.20, L.45 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.45 Hydrogen bonds: C:N.20

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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