› 6i33

X-ray diffraction
2.3Å resolution

Crystal structure of human glycine decarboxylase (P-protein)

Released:
DOI: 10.2210/pdb6i33/pdb
PDB entry 6i33 coloured by chain, front view.
PDB entry 6i33 coloured by chain, side view.
PDB entry 6i33 coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Van Laer B, Kapp U, Leonard G, Mueller-Dieckmann C

Function and Biology Details

Reaction catalysed: 
Glycine + [glycine-cleavage complex H protein]-N(6)-lipoyl-L-lysine = [glycine-cleavage complex H protein]-S-aminomethyl-N(6)-dihydrolipoyl-L-lysine + CO(2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-149943 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Glycine dehydrogenase (decarboxylating), mitochondrial Chains: A, B
Molecule details ›
Chains: A, B
Length: 984 amino acids
Theoretical weight: 109.51 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P23378 (Residues: 45-1020; Coverage: 96%)
Gene names: GCSP, GLDC
Sequence domains:

Ligands and Environments


Cofactor: Ligand PLP 2 x PLP
2 bound ligands:
Ligand EDO 9 x EDO
Ligand BCT 1 x BCT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE MASSIF-3
Spacegroup: P21
Unit cell:
a: 85.81Å b: 123.51Å c: 99.51Å
α: 90° β: 97.87° γ: 90°
R-values:
R R work R free
0.213 0.212 0.235
Expression system: Escherichia coli BL21(DE3)

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