› 8td6

X-ray diffraction
2.08Å resolution

Structure of PYCR1 complexed with NADH and 2-(Methylthio)acetic acid

Released:
DOI: 10.2210/pdb8td6/pdb
PDB entry 8td6 coloured by chain, front view.
PDB entry 8td6 coloured by chain, side view.
PDB entry 8td6 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Screening a knowledge-based library of low molecular weight compounds against the proline biosynthetic enzyme 1-pyrroline-5-carboxylate 1 (PYCR1).
Meeks KR, Bogner AN, Tanner JJ
Protein Sci 33 e5072 (2024)
PMID: 39133178

Function and Biology Details

Reaction catalysed: 
L-proline + NAD(P)(+) = 1-pyrroline-5-carboxylate + NAD(P)H
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
homo decamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-152259 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Pyrroline-5-carboxylate reductase 1, mitochondrial Chains: A, B, C, D, E
Molecule details ›
Chains: A, B, C, D, E
Length: 316 amino acids
Theoretical weight: 33.53 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P32322 (Residues: 1-294; Coverage: 92%)
  • Best match: P32322-3 (Residues: 27-321)
Gene name: PYCR1
Sequence domains:

Ligands and Environments


Cofactor: Ligand NAI 5 x NAI
2 bound ligands:
Ligand MTG 4 x MTG
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: C2
Unit cell:
a: 110.578Å b: 178.922Å c: 87.91Å
α: 90° β: 106.72° γ: 90°
R-values:
R R work R free
0.189 0.187 0.222
Expression system: Escherichia coli

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