› 3fgt

X-ray diffraction
2.4Å resolution

Two chain form of the 66.3 kDa protein from mouse lacking the linker peptide

Released:
DOI: 10.2210/pdb3fgt/pdb
PDB entry 3fgt coloured by chain, front view.
PDB entry 3fgt coloured by chain, side view.
PDB entry 3fgt coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Initial insight into the function of the lysosomal 66.3 kDa protein from mouse by means of X-ray crystallography.
Lakomek K, Dickmanns A, Kettwig M, Urlaub H, Ficner R, Lübke T
BMC Struct Biol 9 56 (2009)
PMID: 19706171

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-174811 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (3 distinct):
Putative phospholipase B-like 2 28 kDa form Chain: A
Molecule details ›
Chain: A
Length: 202 amino acids
Theoretical weight: 22.77 KDa
Source organism: Mus musculus
Expression system: Homo sapiens
UniProt:
  • Canonical: Q3TCN2 (Residues: 47-248; Coverage: 37%)
Gene name: Plbd2
Sequence domains: Phospholipase B
Structure domains:
Putative phospholipase B-like 2 40 kDa form Chain: B
Molecule details ›
Chain: B
Length: 357 amino acids
Theoretical weight: 40.48 KDa
Source organism: Mus musculus
Expression system: Homo sapiens
UniProt:
  • Canonical: Q3TCN2 (Residues: 249-594; Coverage: 63%)
Gene name: Plbd2
Sequence domains: Phospholipase B
Structure domains: Penicillin V Acylase; Chain A

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
6 bound ligands:
Ligand NAG 2 x NAG
Ligand ACT 3 x ACT
Ligand GOL 5 x GOL
Ligand PG4 2 x PG4
Ligand NA 1 x NA
Ligand 7PE 1 x 7PE
1 modified residue:
Ligand OCS 1 x OCS

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE X13
Spacegroup: C2
Unit cell:
a: 145.57Å b: 88.22Å c: 63.27Å
α: 90° β: 98.1° γ: 90°
R-values:
R R work R free
0.168 0.166 0.207
Expression system: Homo sapiens

Quick links

Citations

2 review citations

The proteome of lysosomes.
Schröder et al. (2010)
1 more

1 mention without citation

Initial insight into the function of the lysosomal 66.3 kDa protein from mouse by means of X-ray crystallography.
Lakomek et al. (2009)