› 1itu

X-ray diffraction
2Å resolution

HUMAN RENAL DIPEPTIDASE COMPLEXED WITH CILASTATIN

Released:
DOI: 10.2210/pdb1itu/pdb
PDB entry 1itu coloured by chain, front view.
PDB entry 1itu coloured by chain, side view.
PDB entry 1itu coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structure of human renal dipeptidase involved in beta-lactam hydrolysis.
Nitanai Y, Satow Y, Adachi H, Tsujimoto M
J Mol Biol 321 177-84 (2002)
PMID: 12144777

Function and Biology Details

Reactions catalysed: 
Hydrolysis of dipeptides.
A beta-lactam + H(2)O = a substituted beta-amino acid
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-147727 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Dipeptidase 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 369 amino acids
Theoretical weight: 41.11 KDa
Source organism: Homo sapiens
Expression system: Komagataella pastoris
UniProt:
  • Canonical: P16444 (Residues: 17-385; Coverage: 93%)
Gene names: DPEP1, MDP, RDP
Sequence domains: Membrane dipeptidase (Peptidase family M19)
Structure domains: Metal-dependent hydrolases

Ligands and Environments

3 bound ligands:
Ligand NAG 4 x NAG
Ligand ZN 4 x ZN
Ligand CIL 2 x CIL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU300
Spacegroup: P21
Unit cell:
a: 80.179Å b: 79.491Å c: 56.951Å
α: 90° β: 96.34° γ: 90°
R-values:
R R work R free
0.191 0.185 0.254
Expression system: Komagataella pastoris

Quick links

Citations

4 review citations

Inborn errors in the metabolism of glutathione.
Ristoff et al. (2007)
3 more

3 mentions without citation

Gene composer: database software for protein construct design, codon engineering, and gene synthesis.
Lorimer et al. (2009)
2 more