› 3ebq

X-ray diffraction
1.9Å resolution

Crystal structure of human PPPDE1

Released:
DOI: 10.2210/pdb3ebq/pdb
PDB entry 3ebq coloured by chain, front view.
PDB entry 3ebq coloured by chain, side view.
PDB entry 3ebq coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Walker JR, Akutsu M, Qiu L, Li Y, Slessarev Y, Bountra C, Weigelt J, Arrowsmith CH, Edwards AM, Botchkarev A, Dhe-Paganon S, Structural Genomics Consortium (SGC)

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-179754 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Desumoylating isopeptidase 1 Chain: A
Molecule details ›
Chain: A
Length: 170 amino acids
Theoretical weight: 18.42 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6ICB0 (Residues: 1-168; Coverage: 100%)
Gene names: DESI1, FAM152B, PPPDE2
Sequence domains: PPPDE putative peptidase domain
Structure domains: PPPDE domains

Ligands and Environments

1 bound ligand:
Ligand HG 2 x HG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E SUPERBRIGHT
Spacegroup: P43212
Unit cell:
a: 41.625Å b: 41.625Å c: 184.239Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.226 0.224 0.273
Expression system: Escherichia coli

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