› 6i35

X-ray diffraction
2Å resolution

Crystal structure of human glycine decarboxylase (P-protein) bound with pyridoxyl-glycine-5'-monophosphate

Released:
DOI: 10.2210/pdb6i35/pdb
PDB entry 6i35 coloured by chain, front view.
PDB entry 6i35 coloured by chain, side view.
PDB entry 6i35 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, C, D
Molecule details ›
Chains: A, B, C, D
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

5 bound ligands:
Ligand PLG 4 x PLG
Ligand EDO 4 x EDO
Ligand GOL 5 x GOL
Ligand BCT 1 x BCT
Ligand PEG 4 x PEG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE MASSIF-3
Spacegroup: P21
Unit cell:
a: 85.66Å b: 123.44Å c: 197.67Å
α: 90° β: 97.93° γ: 90°
R-values:
R R work R free
0.216 0.215 0.24
Expression system: Escherichia coli BL21(DE3)

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