› 5gpg

X-ray diffraction
1.67Å resolution

Co-crystal structure of the FK506 binding domain of human FKBP25, Rapamycin and the FRB domain of human mTOR

Released:
DOI: 10.2210/pdb5gpg/pdb
PDB entry 5gpg coloured by chain, front view.
PDB entry 5gpg coloured by chain, side view.
PDB entry 5gpg coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Proximity-Directed Labeling Reveals a New Rapamycin-Induced Heterodimer of FKBP25 and FRB in Live Cells.
Lee SY, Lee H, Lee HK, Lee SW, Ha SC, Kwon T, Seo JK, Lee C, Rhee HW
ACS Cent Sci 2 506-16 (2016)
PMID: 27610411

Function and Biology Details

Reactions catalysed: 
Peptidylproline (omega=180) = peptidylproline (omega=0)
ATP + a protein = ADP + a phosphoprotein
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-154620 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Peptidyl-prolyl cis-trans isomerase FKBP3 Chain: A
Molecule details ›
Chain: A
Length: 117 amino acids
Theoretical weight: 13.05 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q00688 (Residues: 109-224; Coverage: 52%)
Gene names: FKBP25, FKBP3
Sequence domains: FKBP-type peptidyl-prolyl cis-trans isomerase
Structure domains: Chitinase A; domain 3
Serine/threonine-protein kinase mTOR Chain: B
Molecule details ›
Chain: B
Length: 93 amino acids
Theoretical weight: 11.35 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P42345 (Residues: 2021-2112; Coverage: 4%)
Gene names: FRAP, FRAP1, FRAP2, MTOR, RAFT1, RAPT1
Sequence domains: FKBP12-rapamycin binding domain
Structure domains: FKBP12-rapamycin binding domain

Ligands and Environments

1 bound ligand:
Ligand RAP 1 x RAP
1 modified residue:
Ligand CAS 1 x CAS

Experiments and Validation Details

Entry percentile scores
X-ray source: PAL/PLS BEAMLINE 7A (6B, 6C1)
Spacegroup: P212121
Unit cell:
a: 46.038Å b: 58.352Å c: 86.502Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.176 0.174 0.212
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 review citations

Proximity Dependent Biotinylation: Key Enzymes and Adaptation to Proteomics Approaches.
Samavarchi-Tehrani et al. (2020)
3 more

8 mentions without citation

Rational design of small-molecule responsive protein switches.
Shui et al. (2023)
7 more