SMTL ID : 7ns5.1

Structure of yeast Fbp1 (Fructose-1,6-bisphosphatase 1)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

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

PO4.1: 8 residues within 4Å: Chain A: E.108, D.128, I.130, D.131, G.132, S.133 Ligands: MG.2, MG.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.108, A:E.108, A:D.131, A:G.132, A:S.133 Water bridges: A:S.133 PO4.4: 8 residues within 4Å: Chain B: E.108, D.128, I.130, D.131, G.132, S.133 Ligands: MG.5, MG.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.108, B:G.132, B:S.133 PO4.7: 8 residues within 4Å: Chain C: E.108, D.128, I.130, D.131, G.132, S.133 Ligands: MG.8, MG.9 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.108, C:G.132, C:S.133 Water bridges: C:S.133 PO4.10: 8 residues within 4Å: Chain D: E.108, D.128, I.130, D.131, G.132, S.133 Ligands: MG.11, MG.12 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.131, D:G.132, D:S.133 Water bridges: D:S.133

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: E.108, D.128, D.131, E.292 Ligands: PO4.1, MG.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.108, A:D.128, A:D.131, A:E.292, H2O.1 MG.3: 6 residues within 4Å: Chain A: E.108, D.128, I.130, D.131 Ligands: PO4.1, MG.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.108, A:D.128, A:D.128, A:I.130, H2O.1 MG.5: 5 residues within 4Å: Chain B: E.108, D.128, D.131, E.292 Ligands: PO4.4 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.108, B:D.128, B:D.131, B:E.292, H2O.5 MG.6: 6 residues within 4Å: Chain B: E.108, E.109, D.128, I.130, D.131 Ligands: PO4.4 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.128, B:I.130, H2O.4 MG.8: 6 residues within 4Å: Chain C: E.108, D.128, D.131, E.292 Ligands: PO4.7, MG.9 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.108, C:D.128, C:D.131, C:E.292, H2O.6 MG.9: 7 residues within 4Å: Chain C: E.108, E.109, D.128, I.130, D.131 Ligands: PO4.7, MG.8 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.108, C:D.128, C:D.128, C:I.130, H2O.6 MG.11: 5 residues within 4Å: Chain D: E.108, D.128, D.131, E.292 Ligands: PO4.10 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.108, D:D.128, D:D.131, D:E.292, H2O.9 MG.12: 6 residues within 4Å: Chain D: E.108, E.109, D.128, I.130, D.131 Ligands: PO4.10 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.108, D:D.128, D:D.128, D:I.130, H2O.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sherpa, D. et al., GID E3 ligase supramolecular chelate assembly configures multipronged ubiquitin targeting of an oligomeric metabolic enzyme. Mol.Cell (2021)

Release Date

2021-05-05

Peptides

Fructose-1,6-bisphosphatase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
B

D
C

Fructose-1,6-bisphosphatase