› 5jtc

X-ray diffraction
2.24Å resolution

Aspartyl/Asparaginyl beta-hydroxylase (AspH)oxygenase and TPR domains in complex with manganese, 2,4-pyridine dicarboxylate and factor X substrate peptide fragment(39mer-4Ser)

Released:
DOI: 10.2210/pdb5jtc/pdb
PDB entry 5jtc coloured by chain, front view.
PDB entry 5jtc coloured by chain, side view.
PDB entry 5jtc coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Aspartate/asparagine-β-hydroxylase: a high-throughput mass spectrometric assay for discovery of small molecule inhibitors.
Brewitz L, Tumber A, Pfeffer I, McDonough MA, Schofield CJ
Sci Rep 10 8650 (2020)
PMID: 32457455

Function and Biology Details

Reactions catalysed: 
Peptide L-aspartate + 2-oxoglutarate + O(2) = peptide 3-hydroxy-L-aspartate + succinate + CO(2)
Selective cleavage of Arg-|-Thr and then Arg-|-Ile bonds in prothrombin to form thrombin.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133217 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Aspartyl/asparaginyl beta-hydroxylase Chain: A
Molecule details ›
Chain: A
Length: 429 amino acids
Theoretical weight: 49.41 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q12797 (Residues: 330-758; Coverage: 57%)
Gene names: ASPH, BAH
Sequence domains:
Structure domains: B-lactam Antibiotic, Isopenicillin N Synthase; Chain
Factor X light chain Chain: B
Molecule details ›
Chain: B
Length: 39 amino acids
Theoretical weight: 4.19 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P00742 (Residues: 86-124; Coverage: 9%)
Gene name: F10
Sequence domains: EGF-like domain

Ligands and Environments

4 bound ligands:
Ligand MN 1 x MN
Ligand PD2 1 x PD2
Ligand BR 1 x BR
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P212121
Unit cell:
a: 50.02Å b: 91.66Å c: 123.05Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.183 0.181 0.208
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

7 citation in other articles

Mass spectrometry reveals potential of β-lactams as SARS-CoV-2 Mpro inhibitors.
Malla et al. (2021)
6 more

5 mentions without citation

Synthesis of Novel Pyridine-Carboxylates as Small-Molecule Inhibitors of Human Aspartate/Asparagine-β-Hydroxylase.
Brewitz et al. (2020)
4 more