› 6fdw

X-ray diffraction
1.96Å resolution

Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-356

Released:
DOI: 10.2210/pdb6fdw/pdb
PDB entry 6fdw coloured by chain, front view.
PDB entry 6fdw coloured by chain, side view.
PDB entry 6fdw coloured by chain, top view.
Source organism: Trypanosoma brucei
Entry authors: Singh AK, Brown DG

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-186683 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Phosphodiesterase Chains: A, B
Molecule details ›
Chains: A, B
Length: 360 amino acids
Theoretical weight: 40.62 KDa
Source organism: Trypanosoma brucei
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8WQX9 (Residues: 565-918; Coverage: 38%)
Gene name: PDEB1
Sequence domains: 3'5'-cyclic nucleotide phosphodiesterase
Structure domains: 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain

Ligands and Environments

5 bound ligands:
Ligand D62 2 x D62
Ligand ZN 2 x ZN
Ligand MG 2 x MG
Ligand GAI 1 x GAI
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: C2
Unit cell:
a: 111.69Å b: 119.26Å c: 67.97Å
α: 90° β: 108.38° γ: 90°
R-values:
R R work R free
0.192 0.19 0.237
Expression system: Escherichia coli BL21(DE3)

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