SMTL ID : 6m1b.1

A new V27M variant of beta 2 microglobulin induced amyloidosis in a patient with long-term hemodialysis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-dimer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: M.1, I.2, Q.3, P.33, V.86 No protein-ligand interaction detected (PLIP) GOL.2: 3 residues within 4Å: Chain A: I.2, Q.3, R.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.4, A:R.4 GOL.6: 5 residues within 4Å: Chain B: M.1, I.2, Q.3, P.33, V.86 No protein-ligand interaction detected (PLIP) GOL.7: 3 residues within 4Å: Chain B: I.2, Q.3, R.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.4, B:R.4

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: H.85, V.86, L.88 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.85, A:L.88, H2O.1, H2O.1 MG.8: 3 residues within 4Å: Chain B: H.85, V.86, L.88 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.85, B:L.88, H2O.1, H2O.2

2 x CA: CALCIUM ION(Non-functional Binders)

CA.4: 3 residues within 4Å: Ligands: PO4.5, CA.9, PO4.10 No protein-ligand interaction detected (PLIP) CA.9: 3 residues within 4Å: Ligands: CA.4, PO4.5, PO4.10 No protein-ligand interaction detected (PLIP)

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 9 residues within 4Å: Chain A: Q.9, Y.11, R.13, Y.27, M.100 Chain B: Y.27 Ligands: CA.4, CA.9, PO4.10 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.9, A:Y.11, A:Y.11, B:Y.27 Water bridges: A:R.13, B:Y.27 Salt bridges: A:R.13 PO4.10: 9 residues within 4Å: Chain A: Y.27 Chain B: Q.9, Y.11, R.13, Y.27, M.100 Ligands: CA.4, PO4.5, CA.9 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.9, B:Y.11, B:Y.11, A:Y.27 Water bridges: B:R.13, A:Y.27 Salt bridges: B:R.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mizuno, H. et al., Dialysis-related amyloidosis associated with a novel beta 2 -microglobulin variant. Amyloid (2021)

Release Date

2021-01-06

Peptides

Beta-2-microglobulin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Beta-2-microglobulin