› 3c5q

X-ray diffraction
2.4Å resolution

Crystal structure of diaminopimelate decarboxylase (I148L mutant) from Helicobacter pylori complexed with L-lysine

Released:
DOI: 10.2210/pdb3c5q/pdb
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PDB entry 3c5q coloured by chain, front view.
PDB entry 3c5q coloured by chain, side view.
PDB entry 3c5q coloured by chain, top view.
Source organism: Helicobacter pylori SS1
Entry authors: Hu T, Wu D, Jiang H, Shen X

Function and Biology Details

Reaction catalysed: 
Meso-2,6-diaminoheptanedioate = L-lysine + CO(2)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-110150 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Diaminopimelate decarboxylase Chain: A
Molecule details ›
Chain: A
Length: 425 amino acids
Theoretical weight: 47.47 KDa
Source organism: Helicobacter pylori SS1
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: B4XMC6 (Residues: 1-405; Coverage: 100%)
Gene name: lysA
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand PLP 1 x PLP
2 bound ligands:
Ligand LYS 1 x LYS
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: RIGAKU
Spacegroup: P3221
Unit cell:
a: 79.111Å b: 79.111Å c: 134.821Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.202 0.202 0.253
Expression system: Escherichia coli BL21

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