SMTL ID : 7qnw.1

The receptor binding domain of SARS-CoV-2 Omicron variant spike glycoprotein in complex with Beta-55 and EY6A Fabs

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

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

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 4 residues within 4Å: Chain C: F.12, D.13, N.17, L.42 No protein-ligand interaction detected (PLIP)

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 12 residues within 4Å: Chain A: F.174, P.175, A.176, V.177, S.185, L.186, S.187 Chain B: Q.161, S.163, S.177, S.178, T.179 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.187, A:S.187, B:S.177, B:T.179 GOL.3: 6 residues within 4Å: Chain B: Q.37, Q.38, K.39, K.42, A.43, K.45 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.39, B:K.42, B:K.42 GOL.4: 7 residues within 4Å: Chain B: Q.37, K.45, P.59, R.61, F.62, E.81, D.82 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.37, B:K.45, B:K.45, B:R.61, B:D.82 GOL.5: 6 residues within 4Å: Chain C: T.50, G.78, V.81, V.177, Y.182 Chain D: Y.105 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.105, D:Y.105 GOL.7: 8 residues within 4Å: Chain D: S.7, G.8, P.9, G.10, T.121, M.122, P.163, K.215 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.8, D:G.8, D:T.121 GOL.8: 8 residues within 4Å: Chain D: Y.159, E.162, P.163, V.164, F.180, P.181, A.182, L.192 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.162, D:V.164, D:V.164, D:A.182 GOL.9: 3 residues within 4Å: Chain C: R.82 Chain D: Y.105, Y.106 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:R.82, D:Y.106, D:Y.106 Water bridges: D:Y.105 GOL.10: 4 residues within 4Å: Chain D: F.72, V.73, D.74, T.75 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.74, D:T.75 GOL.13: 11 residues within 4Å: Chain D: F.180, P.181, V.183, S.191, L.192, S.193 Chain E: Q.161, S.163, S.177, S.178, T.179 7 PLIP interactions: 4 interactions with chain E, 3 interactions with chain D Hydrogen bonds: E:Q.161, E:S.163, E:S.177, E:T.179, D:F.180, D:S.191, D:S.193

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 4 residues within 4Å: Chain C: G.159, Y.163, F.164, R.167 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Y.163 Hydrogen bonds: C:F.164 Salt bridges: C:R.167 ACT.11: 4 residues within 4Å: Chain D: N.108 Chain E: S.30, W.32, I.92 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.30

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

CL.12: 5 residues within 4Å: Chain D: E.48, W.49, N.62 Chain E: W.97, T.98 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dejnirattisai, W. et al., SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses. Cell (2022)

Release Date

2022-01-19

Peptides

EY6A heavy chain: A
EY6A light chain: B
Surface glycoprotein: C
Beta-55 heavy chain: D
Beta-55 light chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
E

D
A

E
B

EY6A heavy chain

EY6A light chain

Surface glycoprotein

Beta-55 heavy chain

Beta-55 light chain

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