SMTL ID : 7fcp.1

Crystallographic structure of two neutralizing antibodies in complex with SARS-CoV-2 spike receptor-binding Domain (RBD)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

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

Ligands

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.1: 6 residues within 4Å: Chain A: S.57, T.58, G.86, V.89, R.90, Y.190 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.57, A:T.58, A:G.86, A:R.90 Water bridges: A:V.89

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

NAG.2: 2 residues within 4Å: Chain A: N.25, V.49 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.25

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain B: G.66, R.67, V.68, S.69, S.84 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.68, B:S.84, B:S.84 Water bridges: B:G.66 GOL.4: 11 residues within 4Å: Chain D: F.173, P.174, V.176, S.184, L.185, S.186 Chain E: Q.160, S.162, S.176, S.177, T.178 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain E Hydrogen bonds: D:S.186, E:S.162, E:S.177, E:T.178 Water bridges: E:Q.160

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zou, J. et al., Ultrapotent neutralizing antibodies against SARS-CoV-2 with a high degree of mutation resistance. J.Clin.Invest. (2022)

Release Date

2022-06-15

Peptides

Spike protein S1: A
P14-44 antibody Fab fragment heavy chain: B
P14-44 antibody Fab fragment light chain: C
P5-22 antibody Fab fragment heavy chain: D
P5-22 antibody Fab fragment light chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

D
B

E
D

Spike protein S1

P14-44 antibody Fab fragment heavy chain

P14-44 antibody Fab fragment light chain

P5-22 antibody Fab fragment heavy chain

P5-22 antibody Fab fragment light chain

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