SMTL ID : 7u2e.1

Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody ADI-55688

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: G.7, F.10, N.11, V.35, L.36 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.10, A:L.36 Hydrogen bonds: A:N.11

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

SO4.2: 4 residues within 4Å: Chain A: R.71, Y.173 Chain B: S.31, S.53 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Y.173, B:S.53, B:S.53 Salt bridges: A:R.71 SO4.3: 3 residues within 4Å: Chain B: F.27, T.28, Y.32 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.28, B:T.28, B:T.28, B:Y.32 SO4.4: 5 residues within 4Å: Chain B: F.27, T.28, F.29, S.30, N.77 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.29, B:S.30, B:S.30, B:N.77 SO4.5: 3 residues within 4Å: Chain B: S.63, K.65, R.87 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.65, B:R.87 SO4.6: 5 residues within 4Å: Chain B: Q.182, S.183 Chain C: G.164, E.166, S.185 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:S.185, B:S.183, B:S.183 SO4.7: 7 residues within 4Å: Chain B: R.38, Q.39, A.40, K.43, G.44, L.45, E.46 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.38, B:A.40 SO4.8: 3 residues within 4Å: Chain C: Q.1, S.25, S.27 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.25, C:S.27, C:S.27 SO4.9: 4 residues within 4Å: Chain C: P.170, S.171, K.172, Y.178 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.172 SO4.10: 4 residues within 4Å: Chain B: V.174, H.175 Chain C: Q.173, S.174 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:S.174, C:S.174 Salt bridges: B:H.175

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yuan, M. et al., A broad and potent neutralization epitope in SARS-related coronaviruses. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-05-04

Peptides

Spike protein S1: A
ADI-55688 heavy chain: B
ADI-55688 light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

Spike protein S1

ADI-55688 heavy chain

ADI-55688 light chain

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