SMTL ID : 9m7m.1

Crystal structure of human pseudouridine 5'-monophosphate phosphatase (hHDHD1A) complexed with pseudouridine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.26 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.12, D.14, E.173, D.174, A.175 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.12, A:D.14, A:D.174, H2O.1, H2O.2, H2O.5

1 x FJF: 5-[(2~{S},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-1~{H}-pyrimidine-2,4-dione(Non-covalent)

FJF.2: 17 residues within 4Å: Chain A: D.14, E.21, Y.24, F.28, Y.39, K.44, V.47, M.48, G.49, K.50, K.51, A.52, A.55, I.59, S.112, S.113, K.121 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:E.21, A:E.21, A:Y.39, A:Y.39, A:K.44, A:G.49, A:K.50, A:K.51 Water bridges: A:E.21, A:E.21, A:Y.24, A:A.52, A:A.56, A:A.56, A:G.114 pi-Stacking: A:Y.24

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Seo, S. et al., Structural and functional insights into the substrate specificity of the pseudouridine monophosphate phosphatase HDHD1A. J.Biol.Chem. (2025)

Release Date

2025-06-18

Peptides

Pseudouridine-5'-phosphatase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Pseudouridine-5'-phosphatase

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