SMTL ID : 6yxk.1

Crystal structure of ACPA 3F3 in complex with cit-vimentin 59-74

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: F.59, V.67, N.68, T.70 No protein-ligand interaction detected (PLIP) NAG.2: 6 residues within 4Å: Chain A: G.25, Y.26, I.27, S.74, V.75, N.76 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.26 Water bridges: A:F.28, A:F.28, A:N.76, A:N.76 NAG.3: 7 residues within 4Å: Chain B: T.20, N.22, S.71, G.72, D.76, F.77, N.78 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.76, B:N.78 Water bridges: B:T.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kissel, T. et al., Surface Ig variable domain glycosylation affects autoantigen binding and acts as threshold for human autoreactive B cell activation. Sci Adv (2022)

Release Date

2021-05-12

Peptides

ACPA 3F3 Fab fragment - heavy chain: A
ACPA 3F3 Fab fragment - light chain: B
Citrullinated Vimentin (59-74): C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

ACPA 3F3 Fab fragment - heavy chain

ACPA 3F3 Fab fragment - light chain

Citrullinated Vimentin (59-74)