SMTL ID : 7u2d.1

Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody ADG20

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.76 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: F.6, G.7, F.10, N.11, V.35 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.10 Hydrogen bonds: A:N.11

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

SO4.2: 3 residues within 4Å: Chain A: R.71, Q.161 Chain B: E.53 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.161, B:E.53 Salt bridges: A:R.71 SO4.3: 4 residues within 4Å: Chain B: G.26, F.27, T.28, Y.32 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: 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:N.77, B:N.77 SO4.5: 5 residues within 4Å: Chain B: V.174, H.175, T.176 Chain C: Q.173, S.174 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:T.176, B:T.176, C:Q.173 Salt bridges: B:H.175 SO4.6: 3 residues within 4Å: Chain B: S.63, K.65, R.87 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.63 Water bridges: B:R.67 Salt bridges: B:K.65, B:R.87

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.7: 3 residues within 4Å: Chain C: K.108, K.172, Y.178 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:K.108 Hydrogen bonds: C:K.172 Salt bridges: C:K.108, C:K.108, C:K.108

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
ADG20 heavy chain: B
ADG20 light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

Spike protein S1

ADG20 heavy chain

ADG20 light chain

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