› 6oqa

X-ray diffraction
2.2Å resolution

Crystal structure of CEP250 bound to FKBP12 in the presence of FK506-like novel natural product

Released:
DOI: 10.2210/pdb6oqa/pdb
Model geometry
Fit model/data
PDB entry 6oqa coloured by chain, front view.
PDB entry 6oqa coloured by chain, side view.
PDB entry 6oqa coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Genomic discovery of an evolutionarily programmed modality for small-molecule targeting of an intractable protein surface.
Shigdel UK, Lee SJ, Sowa ME, Bowman BR, Robison K, Zhou M, Pua KH, Stiles DT, Blodgett JAV, Udwary DW, Rajczewski AT, Mann AS, Mostafavi S, Hardy T, Arya S, Weng Z, Stewart M, Kenyon K, Morgenstern JP, Pan E, Gray DC, Pollock RM, Fry AM, Klausner RD, Townson SA, Verdine GL
OpenAccess logo Proc Natl Acad Sci U S A 117 17195-17203 (2020)
PMID: 32606248

Function and Biology Details

Reaction catalysed: 
Peptidylproline (omega=180) = peptidylproline (omega=0)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-158815 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Peptidyl-prolyl cis-trans isomerase FKBP1A Chains: A, B, E, F
Molecule details ›
Chains: A, B, E, F
Length: 108 amino acids
Theoretical weight: 11.97 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P62942 (Residues: 1-108; Coverage: 100%)
Gene names: FKBP1, FKBP12, FKBP1A
Sequence domains: FKBP-type peptidyl-prolyl cis-trans isomerase
Centrosome-associated protein CEP250 Chains: C, D, G, H
Molecule details ›
Chains: C, D, G, H
Length: 98 amino acids
Theoretical weight: 11.43 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9BV73 (Residues: 2134-2231; Coverage: 4%)
Gene names: CEP2, CEP250, CNAP1

Ligands and Environments

8 bound ligands:
Ligand 60Z 4 x 60Z
Ligand EDO 16 x EDO
Ligand PEG 10 x PEG
Ligand PE8 2 x PE8
Ligand PGE 4 x PGE
Ligand PG4 4 x PG4
Ligand MG 1 x MG
Ligand MLA 1 x MLA
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: APS BEAMLINE 21-ID-G
Spacegroup: P21
Unit cell:
a: 60.832Å b: 64.952Å c: 136.055Å
α: 90° β: 90.46° γ: 90°
R-values:
R R work R free
0.21 0.208 0.256
Expression systems:
  • Not provided
  • Escherichia coli

Quick links

Citations

8 review citations

Mining genomes to illuminate the specialized chemistry of life.
Medema et al. (2021)
7 more

2 mentions without citation

Protein-protein interfaces in molecular glue-induced ternary complexes: classification, characterization, and prediction.
Rui et al. (2023)
1 more