› 3fgr

X-ray diffraction
1.8Å resolution

Two chain form of the 66.3 kDa protein at 1.8 Angstroem

Released:
DOI: 10.2210/pdb3fgr/pdb
PDB entry 3fgr coloured by chain, front view.
PDB entry 3fgr coloured by chain, side view.
PDB entry 3fgr 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
5 bound ligands:
Ligand NAG 3 x NAG
Ligand GOL 11 x GOL
Ligand ACT 2 x ACT
Ligand XE 1 x XE
Ligand NA 1 x NA
1 modified residue:
Ligand OCS 1 x OCS

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.2
Spacegroup: C2
Unit cell:
a: 148.737Å b: 89.56Å c: 64.811Å
α: 90° β: 98.69° γ: 90°
R-values:
R R work R free
0.153 0.152 0.182
Expression system: Homo sapiens

Quick links

Citations

1 review citation

The proteome of lysosomes.
Schröder et al. (2010)
8 other articles

5 mentions without citation

Water in Nanopores and Biological Channels: A Molecular Simulation Perspective.
Lynch et al. (2020)
4 more