SMTL ID : 7s5r.1

Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibodies CV07-287 and COVA1-16

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

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

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: F.111, T.112, F.146, S.196, F.197, E.198 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.112, A:F.197 Water bridges: A:T.112 EDO.2: 2 residues within 4Å: Chain A: G.128, G.129 No protein-ligand interaction detected (PLIP) EDO.3: 3 residues within 4Å: Chain A: Q.91, G.98, K.99 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.91, A:K.99 EDO.8: 4 residues within 4Å: Chain B: Y.33, R.101, N.102, Y.110 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.102, B:N.102 Water bridges: A:G.63 EDO.9: 1 residues within 4Å: Chain B: R.72 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.72, B:R.72 EDO.10: 6 residues within 4Å: Chain B: R.38, Q.39, A.40, Q.43, G.44, E.46 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.40 EDO.17: 3 residues within 4Å: Chain D: S.137, S.138 Chain E: E.214 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.138, D:S.138 EDO.18: 1 residues within 4Å: Chain D: T.58 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.58, D:T.58 Water bridges: D:T.58

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

NAG.4: 4 residues within 4Å: Chain A: G.21, F.24, N.25, V.49 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.24, A:V.49 Hydrogen bonds: A:N.25

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

SO4.5: 4 residues within 4Å: Chain A: T.182, N.183, G.184, Y.187 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.183, A:G.184 SO4.6: 3 residues within 4Å: Chain A: K.126, N.130, N.132 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.130, A:N.132 Salt bridges: A:K.126 SO4.7: 4 residues within 4Å: Chain A: T.58, K.60, V.89, R.90 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.58 Water bridges: A:R.90, A:R.90 Salt bridges: A:K.60 SO4.11: 7 residues within 4Å: Chain A: Y.62, Q.96 Chain B: P.100, R.101, Y.103, A.113, Y.115 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Y.62, A:Y.62, B:R.101, B:R.101, B:Y.115 Water bridges: A:Q.96, A:Q.96 SO4.12: 4 residues within 4Å: Chain B: V.2, Q.117, H.118, W.119 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.119, B:W.119 Salt bridges: B:H.118 SO4.13: 2 residues within 4Å: Chain B: Y.60, Q.65 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.65, B:Q.65 Water bridges: B:T.58 SO4.14: 4 residues within 4Å: Chain B: V.11, K.13, S.131, T.132 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.132, B:T.132 Salt bridges: B:K.13 SO4.15: 5 residues within 4Å: Chain B: Y.33, I.50, N.52, S.57, T.58 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.52, B:S.57 Water bridges: B:Y.33 SO4.16: 3 residues within 4Å: Chain C: P.8, S.9, S.10 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.9, C:S.9 SO4.19: 5 residues within 4Å: Chain D: F.27, T.28, F.29, T.30, S.77 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:F.29, D:T.30, D:S.77

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
COVA1-16 Heavy chain: B
COVA1-16 Light chain: C
CV07-287 Heavy chain: D
CV07-287 Light chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

D
B

E
C

Spike protein S1

COVA1-16 Heavy chain

COVA1-16 Light chain

CV07-287 Heavy chain

CV07-287 Light chain

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