SMTL ID : 7s5p.1

Crystal structure of SARS-CoV-2 B.1.351 variant receptor binding domain in complex with neutralizing antibody CS23

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.86 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: F.20, G.21, F.24, N.25 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.24 Hydrogen bonds: A:N.25

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

SO4.2: 1 residues within 4Å: Chain A: R.148 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.148 SO4.3: 3 residues within 4Å: Chain A: G.184, V.185 Chain C: N.25 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.185 SO4.4: 4 residues within 4Å: Chain A: Q.180 Chain C: N.64, S.65, G.66 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:N.64, C:G.66, A:Q.180 SO4.5: 4 residues within 4Å: Chain A: P.108, D.109, D.110, P.145 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.109, A:D.110, A:D.110 SO4.6: 5 residues within 4Å: Chain A: S.159 Chain B: E.1, G.26, F.27, N.76 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.159, A:S.159, B:G.26, B:N.76 SO4.7: 3 residues within 4Å: Chain B: H.72, N.73, S.74 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.73, B:S.74 Salt bridges: B:H.72 SO4.8: 4 residues within 4Å: Chain B: R.19, H.72, K.75, Y.79 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.79 Salt bridges: B:R.19, B:H.72, B:K.75 SO4.10: 4 residues within 4Å: Chain C: Y.1, E.2, N.24 Ligands: SO4.15 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.1, C:E.2, C:E.2, C:N.24 SO4.11: 4 residues within 4Å: Chain C: R.52, P.53, S.54, G.55 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.54, C:G.55 Salt bridges: C:R.52 SO4.12: 3 residues within 4Å: Chain C: G.66, N.67, T.68 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.67, C:N.67, C:T.68 SO4.13: 5 residues within 4Å: Chain C: E.81, V.106, Y.141, K.167, Y.173 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.81, C:T.105, C:Y.141, C:Y.173 Salt bridges: C:K.167 SO4.14: 2 residues within 4Å: Chain C: Q.185, H.189 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.185 Salt bridges: C:H.189 SO4.15: 3 residues within 4Å: Chain C: Y.1, E.2 Ligands: SO4.10 No protein-ligand interaction detected (PLIP)

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.9: 3 residues within 4Å: Chain B: V.168, H.169 Chain C: S.169 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.169 EDO.16: 2 residues within 4Å: Chain C: T.16, R.18 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.16, C:R.18, C:R.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Reincke, S.M. et al., SARS-CoV-2 Beta variant infection elicits potent lineage-specific and cross-reactive antibodies. Science (2022)

Release Date

2022-03-09

Peptides

Spike protein S1: A
CS23 Heavy chain: B
CS23 Light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

Spike protein S1

CS23 Heavy chain

CS23 Light chain

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