› 3ly0

X-ray diffraction
1.4Å resolution

Crystal structure of metallo peptidase from Rhodobacter sphaeroides liganded with phosphinate mimic of dipeptide L-Ala-D-Ala

Released:
DOI: 10.2210/pdb3ly0/pdb
PDB entry 3ly0 coloured by chain, front view.
PDB entry 3ly0 coloured by chain, side view.
PDB entry 3ly0 coloured by chain, top view.
Source organism: Cereibacter sphaeroides 2.4.1
Entry authors: Fedorov AA, Fedorov EV, Cummings J, Raushel FM, Burley SK, Almo SC, New York SGX Research Center for Structural Genomics (NYSGXRC)

Function and Biology Details

Reaction catalysed: 
Hydrolysis of dipeptides.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-174594 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Dipeptidase AC Chains: A, B
Molecule details ›
Chains: A, B
Length: 364 amino acids
Theoretical weight: 40.17 KDa
Source organism: Cereibacter sphaeroides 2.4.1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q3IZQ3 (Residues: 4-354; Coverage: 99%)
Gene name: RSP_0802
Sequence domains: Membrane dipeptidase (Peptidase family M19)
Structure domains: Metal-dependent hydrolases

Ligands and Environments

2 bound ligands:
Ligand LY0 2 x LY0
Ligand ZN 4 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X4A
Spacegroup: P1
Unit cell:
a: 46.649Å b: 50.325Å c: 81.436Å
α: 83.65° β: 73.64° γ: 67.65°
R-values:
R R work R free
0.17 0.169 0.192
Expression system: Escherichia coli

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