› 5sdf

X-ray diffraction
1.88Å resolution

PanDDA analysis group deposition -- Crystal Structure of Porphyromonas gingivalis in complex with Z2856434834

Released:
DOI: 10.2210/pdb5sdf/pdb
PDB entry 5sdf coloured by chain, front view.
PDB entry 5sdf coloured by chain, side view.
PDB entry 5sdf coloured by chain, top view.
Source organism: Porphyromonas gingivalis
Entry authors: Tham CT, Coker JA, Krojer T, Foster WR, Koekemoer L, Douangamath A, Talon R, Fearon D, von Delft F, Yue WW, Bountra C, Bezerra GA

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-109706 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Asp/Glu-specific dipeptidyl-peptidase Chains: A, B
Molecule details ›
Chains: A, B
Length: 707 amino acids
Theoretical weight: 80.75 KDa
Source organism: Porphyromonas gingivalis
Expression system: Escherichia coli
UniProt:
  • Canonical: B2RID1 (Residues: 22-720; Coverage: 100%)
Gene names: PGN_0607, dpp11
Sequence domains: Peptidase S46

Ligands and Environments

2 bound ligands:
Ligand NT7 2 x NT7
Ligand CL 3 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P212121
Unit cell:
a: 101.285Å b: 117.136Å c: 147.78Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.223 0.222 0.248
Expression system: Escherichia coli

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