SMTL ID : 7nx9.1

Crystal structure of the N501Y mutant receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-222 and EY6A Fabs

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

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

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: S.31, Y.32, G.101 Chain C: K.63, D.66 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:S.31 Salt bridges: C:K.63 SO4.2: 5 residues within 4Å: Chain A: Y.32, K.98, G.100, G.101, K.102 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.32, A:Y.32, A:G.101 Water bridges: A:K.98, A:K.102, B:Q.55 Salt bridges: A:K.98, A:K.102 SO4.7: 5 residues within 4Å: Chain C: S.154 Chain D: S.25, G.26, L.27, N.76 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:G.26, D:N.76, C:S.154 Water bridges: C:S.154, C:S.154 SO4.8: 3 residues within 4Å: Chain C: R.134, K.139, E.142 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.136 Salt bridges: C:R.134, C:K.139 SO4.9: 2 residues within 4Å: Chain C: R.34, N.37 3 PLIP interactions: 3 interactions with chain C Water bridges: C:R.34, C:T.70 Salt bridges: C:R.34 SO4.11: 1 residues within 4Å: Chain D: K.123 2 PLIP interactions: 2 interactions with chain D Water bridges: D:G.124 Salt bridges: D:K.123 SO4.12: 1 residues within 4Å: Chain D: K.75 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:K.75 SO4.14: 1 residues within 4Å: Chain E: R.211 2 PLIP interactions: 2 interactions with chain E Salt bridges: E:K.190, E:R.211 SO4.15: 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:R.62, E:R.62 Salt bridges: E:K.40, E:R.46, E:R.62 SO4.16: 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

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 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:T.53, C:Y.185 Water bridges: C:R.85 GOL.5: 5 residues within 4Å: Chain C: D.82, G.181 Chain E: V.2, Q.27, D.93 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.82 Water bridges: C:G.181 GOL.6: 7 residues within 4Å: Chain C: R.80, E.83, Q.86, G.93, K.94 Chain D: Y.52 Chain E: Y.92 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:R.80, C:E.83, C:Q.86, C:K.94 Water bridges: C:T.92, C:K.94, E:Y.92

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

NAG.4: 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

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

PEG.10: 5 residues within 4Å: Chain D: S.7, G.8, G.9, K.207, P.208 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.8

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

CL.13: 5 residues within 4Å: Chain D: Y.151, E.154, P.155, V.156, A.174 Ligand excluded by PLIP

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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