› 6trw

X-ray diffraction
3Å resolution

Crystal structure of DPP8 in complex with the EIL peptide (SLRFLFEGQRIADNH)

Released:
DOI: 10.2210/pdb6trw/pdb
PDB entry 6trw coloured by chain, front view.
PDB entry 6trw coloured by chain, side view.
PDB entry 6trw coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Aerosol-based ligand soaking of reservoir-free protein crystals.
Ross B, Krapp S, Geiss-Friedlander R, Littmann W, Huber R, Kiefersauer R
J Appl Crystallogr 54 895-902 (2021)
PMID: 34188616

Function and Biology Details

Reaction catalysed: 
Release of an N-terminal dipeptide, Xaa-Yaa-|-Zaa-, from a polypeptide, preferentially when Yaa is Pro, provided Zaa is neither Pro nor hydroxyproline.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-159023 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Dipeptidyl peptidase 8 Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 903 amino acids
Theoretical weight: 103.89 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q6V1X1 (Residues: 1-898; Coverage: 100%)
Gene names: DPP8, DPRP1, MSTP097, MSTP135, MSTP141
Sequence domains:
Small ubiquitin-related modifier 1 Chains: D, E, F
Molecule details ›
Chains: D, E, F
Length: 15 amino acids
Theoretical weight: 1.81 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P63165 (Residues: 61-75; Coverage: 15%)
Gene names: OK/SW-cl.43, SMT3C, SMT3H3, SUMO1, UBL1

Ligands and Environments

1 bound ligand:
Ligand NA 3 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: C2221
Unit cell:
a: 163.045Å b: 245.283Å c: 261.439Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.193 0.191 0.226
Expression systems:
  • Spodoptera frugiperda
  • Not provided

Quick links

Citations

1 citations in other articles

LifeSoaks: a tool for analyzing solvent channels in protein crystals and obstacles for soaking experiments.
Pletzer-Zelgert et al. (2023)

1 mention without citation

Aerosol-based ligand soaking of reservoir-free protein crystals.
Ross et al. (2021)