4JFI: Peptidyl-prolyl cis-trans isomerase FKBP5

Name: PDB 4JFI: Increasing the Efficiency Efficiency of Ligands for the FK506-Binding Protein 51 by Conformational Control: Complex of FKBP51 with compound…
Published: 2013-08-28
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: isomerase

Increasing the Efficiency Efficiency of Ligands for the FK506-Binding Protein 51 by Conformational Control: Complex of FKBP51 with compound 1-[(9S,13R,13aR)-1,3-dimethoxy-8-oxo-5,8,9,10,11,12,13,13a-octahydro-6H-9,13-epiminoazocino[2,1-a]isoquinolin-14-yl]-2-(3,4,5-trimethoxyphenyl)ethane-1,2-dione. Determined by X-ray diffraction at 1.05 Å resolution. Released 28 Aug 2013.

Method: X-ray diffraction
Resolution: 1.05 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,273
Mol. weight: 14.59 kDa
Ligands: 1KT
Released: 28 Aug 2013

Explore 4JFI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4JFI contains 6 α-helices and 9 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	14-21	8
α-helix	22	1
β-strand	23-24	2	1
β-strand	33-39	7	1
β-strand	52-61	10	1
β-strand	66-69	4	1
α-helix	71-73	3
β-strand	77-80	4	1
α-helix	88-94	7
α-helix	97-98	2
β-strand	102-107	6	1
α-helix	109-111	3
β-strand	118	1	2
β-strand	122	1	2
β-strand	128-138	11	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Peptidyl-prolyl cis-trans isomerase FKBP5	A	protein	127	Homo sapiens	Q13451 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4JFI_1 Peptidyl-prolyl cis-trans isomerase FKBP5 (chains A)
GAPATVTEQGEDITSKKDRGVLKIVKRVGNGEETPMIGDKVYVHYKGKLSNGKKFDSSHD
RNEPFVFSLGKGQVIKAWDIGVATMKKGEICHLLCKPEYAYGSAGSLPKIPSNATLFFEI
ELLDFKG

Ligands and cofactors

ID	Name	Formula	Copies
1KT	1-[(9S,13R,13aR)-1,3-dimethoxy-8-oxo-5,8,9,10,11,12,13,13a-octahydro-6H-9,13-ep…	C28 H32 N2 O8	1

Water and common crystallization additives (DMS, GOL) are not listed.

Primary citation

Increasing the efficiency of ligands for FK506-binding protein 51 by conformational control. Wang, Y., Kirschner, A., Fabian, A.K. et al. J Med Chem (2013) 56:3922-3935. DOI 10.1021/jm400087k · PubMed

Other PDB entries of the same protein (UniProt Q13451 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7AOT 0.85 Å, The Fk1 domain of FKBP51 in complex with (2R,5S,12R)-12-cyclohexyl-2-[2-(3,4-dimethoxyphe…
7APW 0.89 Å, The Fk1 domain of FKBP51 in complex with (1S,5S,6R)-10-(benzo[d]thiazol-6-ylsulfonyl)-5-(…
8R5K 0.89 Å, The Fk1 domain of FKBP51 in complex with Antascomicine B
7APS 0.94 Å, The Fk1 domain of FKBP51 in complex with (2S)-2-((1S,5R,6R)-10-((3,5-dichlorophenyl)sulfo…
3O5Q 0.96 Å, Fk1 domain mutant A19T of FKBP51, crystal form IV, in presence of DMSO
6TX6 0.98 Å, Crystal structure of human FKBP51 FK1 domain A19T mutant in complex with nicotinamide
8CHN 0.99 Å, The FK1 domain of FKBP51 in complex with (1S,5S,6R)-10-((S)-(3,5-dichlorophenyl)sulfonimi…
3O5P 1.0 Å, Fk1 domain mutant A19T of FKBP51, crystal form IV
4DRQ 1.0 Å, Exploration of Pipecolate Sulfonamides as Binders of the FK506-Binding Proteins 51 and…
5OBK 1.0 Å, The Fk1 domain of FKBP51 in complex with (1S,5S,6R)-10-((3,5-dichlorophenyl)sulfonyl)-5-(…
8CHP 1.0 Å, The FK1 domain of FKBP51 in complex with (1S,5S,6R)-10-((S)-(3,5-dichlorophenyl)sulfinyl)…
8CHQ 1.01 Å, The FK1 domain of FKBP51 in complex with (1S,5S,6R)-10-((S)-3,5-dichloro-N-methylphenylsu…

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