SMTL ID : 8jb3.1

Structure and allosteric regulation of the inosine 5'-monophosphate-specific phosphatase ISN1 from Saccharomyces cerevisiae

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

monomer

Ligands

1 x NOS: INOSINE(Non-covalent)

NOS.1: 12 residues within 4Å: Chain A: D.14, F.16, I.104, G.105, T.106, F.107, L.111, L.143, Q.147, R.422, C.426, T.427 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:D.14, A:G.105, A:Q.147, A:R.422, A:T.427 Water bridges: A:F.16, A:F.108, A:R.422, A:R.422, A:R.422, A:T.427 pi-Stacking: A:F.16 pi-Cation interactions: A:R.422

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

PO4.2: 10 residues within 4Å: Chain A: A.169, G.170, D.171, T.205, A.206, K.381, Q.409, N.417 Ligands: IMP.3, MG.5 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.170, A:D.171, A:D.171, A:T.205, A:T.205, A:T.205, A:A.206, A:Q.409, A:N.417 Salt bridges: A:K.381

1 x IMP: INOSINIC ACID(Non-covalent)

IMP.3: 15 residues within 4Å: Chain A: D.171, D.177, A.206, A.207, G.208, Y.209, R.218, K.314, A.317, F.368, D.373, W.375, D.377 Ligands: PO4.2, MG.4 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:D.171, A:D.177, A:G.208, A:R.218, A:R.218, A:D.377 Water bridges: A:D.171, A:Y.209 Salt bridges: A:R.218 pi-Stacking: A:W.375, A:W.375, A:W.375

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: Y.209, K.314 Ligands: IMP.3 No protein-ligand interaction detected (PLIP) MG.5: 5 residues within 4Å: Chain A: A.169, D.171, D.408, Q.409 Ligands: PO4.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.171, A:D.408, H2O.1, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Byun, S. et al., Structure, cooperativity and inhibition of the inosine 5'-monophosphate-specific phosphatase from Saccharomyces cerevisiae. Febs J. (2024)

Release Date

2024-03-06

Peptides

IMP-specific 5'-nucleotidase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

IMP-specific 5'-nucleotidase 1