SMTL ID : 7afv.1

Crystal structure of tetrameric beta-2-microglobulin deltaN6 S52C stabilized by a covalent ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

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

TRS.1: 5 residues within 4Å: Chain A: Y.21, Y.58 Chain B: Y.5 Ligands: SJK.2, SJK.3 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.5, B:Y.5, A:Y.58 TRS.4: 5 residues within 4Å: Chain C: Y.21, Y.58 Chain D: Y.5 Ligands: SJK.5, SJK.6 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:Y.21, C:Y.58, D:Y.5

4 x SJK: 5-oxidanylidene-~{N}-(2-sulfanylethyl)-2,3-dihydro-[1,3]thiazolo[3,2-a]pyrimidine-6-carboxamide(Non-covalent)

SJK.2: 5 residues within 4Å: Chain A: Y.5, Y.21, C.47 Chain B: Y.21 Ligands: TRS.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.5 pi-Stacking: A:Y.21 SJK.3: 6 residues within 4Å: Chain B: F.17, C.47, L.60, Y.62 Chain D: F.51 Ligands: TRS.1 1 PLIP interactions: 1 interactions with chain B pi-Stacking: B:Y.62 SJK.5: 5 residues within 4Å: Chain C: Y.5, Y.21, C.47 Chain D: Y.21 Ligands: TRS.4 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.21 pi-Stacking: C:Y.21 SJK.6: 6 residues within 4Å: Chain B: F.51 Chain D: F.17, C.47, L.60, Y.62 Ligands: TRS.4 1 PLIP interactions: 1 interactions with chain D pi-Stacking: D:Y.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cawood, E.E. et al., Modulation of Amyloidogenic Protein Self-Assembly Using Tethered Small Molecules. J.Am.Chem.Soc. (2020)

Release Date

2020-12-09

Peptides

Beta-2-microglobulin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Beta-2-microglobulin