4DRH: Peptidyl-prolyl cis-trans isomerase FKBP5

Co-crystal structure of the PPIase domain of FKBP51, Rapamycin and the FRB fragment of mTOR at low pH. Determined by X-ray diffraction at 2.3 Å resolution. Released 6 Feb 2013.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,841
Mol. weight: 58.73 kDa
Ligands: RAP
Released: 6 Feb 2013

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

Secondary structure: helices and β-sheets

4DRH contains 23 α-helices and 18 β-strands across 4 chains. 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: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	14-21	8
β-strand	23-24	2	1
β-strand	33-39	7	1
α-helix	45-48	4
β-strand	52-61	10	1
β-strand	66-68	3	1
α-helix	76	1
β-strand	77-80	4	1
α-helix	88-94	7
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

Chain B: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	2021-2035	15
α-helix	2036-2040	5
α-helix	2041	1
α-helix	2044-2059	16
α-helix	2065-2091	27
α-helix	2095-2111	17

Chain D: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	14-21	8
β-strand	23-24	2	3
β-strand	33-39	7	3
β-strand	52-61	10	3
β-strand	66-68	3	3
α-helix	76	1
β-strand	77-80	4	3
α-helix	88-95	8
β-strand	102-107	6	3
α-helix	109-111	3
β-strand	118	1	4
β-strand	122	1	4
β-strand	128-138	11	3

Chain E: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	2020-2035	16
α-helix	2036-2040	5
α-helix	2041	1
α-helix	2044-2057	14
α-helix	2066-2070	5
α-helix	2071-2075	5
α-helix	2076-2091	16
α-helix	2094-2111	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Peptidyl-prolyl cis-trans isomerase FKBP5	A, D	protein	144	Homo sapiens	Q13451 (AlphaFold model)
Serine/threonine-protein kinase mTOR	B, E	protein	98	Homo sapiens	P42345 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>4DRH_1 Peptidyl-prolyl cis-trans isomerase FKBP5 (chains A, D)
GAMGMTTDEGAKNNEESPTATVAEQGEDITSKKDRGVLKIVKRVGNGEETPMIGDKVYVH
YKGKLSNGKKFDSSHDRNEPFVFSLGKGQVIKAWDIGVATMKKGEICHLLCKPEYAYGSA
GSLPKIPSNATLFFEIELLDFKGE

Sequence of entity 2 (B, E), FASTA

>4DRH_2 Serine/threonine-protein kinase mTOR (chains B, E)
GAMDPEFMEMWHEGLEEASRLYFGERNVKGMFEVLEPLHAMMERGPQTLKETSFNQAYGR
DLMEAQEWCRKYMKSGNVKDLTQAWDLYYHVFRRISKQ

Ligands and cofactors

ID	Name	Formula	Copies
RAP	Rapamycin immunosuppressant drug	C51 H79 N O13	2

Water and common crystallization additives (SO4) are not listed.

Primary citation

Large FK506-Binding Proteins Shape the Pharmacology of Rapamycin. Marz, A.M., Fabian, A.K., Kozany, C. et al. Mol Cell Biol (2013) 33:1357-1367. DOI 10.1128/MCB.00678-12 · 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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