SMTL ID : 7nxb.1

Crystal structure of the receptor binding domain of SARS-CoV-2 P.1 variant Spike glycoprotein in complex with COVOX-222 and EY6A Fabs

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.67 Å

Oligo State

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

Ligands

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

SO4.1: 7 residues within 4Å: Chain A: Y.32, K.98, G.100, G.101, K.102, Y.107, D.109 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.32, A:Y.32, A:G.101, A:K.102 Salt bridges: A:K.98, A:K.102 SO4.4: 4 residues within 4Å: Chain C: S.154 Chain D: S.25, G.26, L.27 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.154, D:G.26 SO4.5: 4 residues within 4Å: Chain C: R.134, N.137, 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 SO4.6: 2 residues within 4Å: Chain C: Y.178 Chain E: S.31 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain E Hydrogen bonds: C:Y.178, E:S.31, E:S.31, E:S.31 SO4.7: 3 residues within 4Å: Chain C: R.34, N.37, N.71 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.37, C:N.71 Salt bridges: C:R.34 SO4.10: 3 residues within 4Å: Chain D: G.86, A.87, E.88 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.87, D:E.88 SO4.11: 1 residues within 4Å: Chain E: R.211 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:R.211 SO4.12: 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 SO4.13: 1 residues within 4Å: Chain E: R.24 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:R.24 SO4.14: 3 residues within 4Å: Chain E: K.103, D.105, R.142 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:D.105 Water bridges: E:R.142 Salt bridges: E:K.103, E:R.142 SO4.15: 3 residues within 4Å: Chain E: K.40, Q.43, R.46 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:Q.38 Water bridges: E:Q.38 Salt bridges: E:K.40, E:R.46 SO4.16: 3 residues within 4Å: Chain E: S.121, D.122, E.123 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:D.122, E:E.123 SO4.17: 4 residues within 4Å: Chain E: P.60, D.61, R.62, R.78 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:D.61, E:R.62 Salt bridges: E:R.62, E:R.78 SO4.18: 2 residues within 4Å: Chain E: R.18, R.78 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:R.18 SO4.19: 6 residues within 4Å: Chain D: Q.39 Chain E: Q.39, K.40, P.41, G.42, Q.43 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:K.40, E:G.42, E:Q.43 Water bridges: D:Q.39

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain C: S.52, T.53, G.81, D.82, Y.185 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.53, C:D.82, C:D.82 GOL.9: 8 residues within 4Å: Chain C: R.80, E.83, T.94, Y.130, L.132 Chain D: E.99, S.101 Chain E: Y.92 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:R.80, C:T.94, D:E.99, D:S.101, D:N.104

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

NAG.3: 4 residues within 4Å: Chain C: F.15, G.16, N.20, L.45 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.45 Hydrogen bonds: C:N.20

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

PEG.8: 5 residues within 4Å: Chain D: G.8, G.9, G.10, K.207, P.208 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.8, D:G.9

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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