8PDF: FKBP12

FKBP12 in complex with PROTAC 6a2. Determined by X-ray diffraction at 1.2 Å resolution. Released 15 Nov 2023.

Method: X-ray diffraction
Resolution: 1.2 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,061
Mol. weight: 12.88 kDa
Ligands: Y5Q
Released: 15 Nov 2023

Explore 8PDF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8PDF contains 5 α-helices and 8 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: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	1
α-helix	20	1
β-strand	21-30	10	1
β-strand	35-38	4	1
β-strand	46-49	4	1
α-helix	57-62	6
α-helix	63-65	3
α-helix	66-67	2
β-strand	71-76	6	1
α-helix	78-80	3
β-strand	87	1	2
β-strand	91	1	2
β-strand	97-106	10	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Peptidyl-prolyl cis-trans isomerase FKBP1A	A	protein	107	Homo sapiens	P62942 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8PDF_1 Peptidyl-prolyl cis-trans isomerase FKBP1A (chains A)
GVQVETISPGDGRTFPKRGQTVVVHYTGMLEDGKKFDSSRDRNKPFKFMLGKQEVIRGWE
EGVAQMSVGQRAKLTISPDYAYGATGHPGIIPPHATLVFDVELLKLE

Ligands and cofactors

ID	Name	Formula	Copies
Y5Q	(2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[4-[(1~{S})-1-[(1~{S},5~{S},6~{R})-10-[3,5-…	C48 H61 Cl2 N9 O9 S2	1

Primary citation

Discovery of a Potent Proteolysis Targeting Chimera Enables Targeting the Scaffolding Functions of FK506-Binding Protein 51 (FKBP51). Geiger, T.M., Walz, M., Meyners, C. et al. Angew Chem Int Ed Engl (2024) 63:e202309706-e202309706. DOI 10.1002/anie.202309706 · PubMed

Other PDB entries of the same protein (UniProt P62942 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2PPN 0.92 Å, Crystal structure of FKBP12
2PPP 0.94 Å, Crystal structure of E60Q mutant of FKBP12
6YF3 1.0 Å, FKBP12 in complex with the BMP potentiator compound 10 at 1.00A resolution
6YF2 1.03 Å, FKBP12 in complex with the BMP potentiator compound 6 at 1.03A resolution
8X6P 1.05 Å, Isomerase Protein
6YF1 1.12 Å, FKBP12 in complex with the BMP potentiator compound 8 at 1.12A resolution
8CHM 1.12 Å, Human FKBP12 in complex with (1S,5S,6R)-10-((S)-(3,5-dichlorophenyl)sulfinyl)-3-(pyridin-…
4N19 1.2 Å, Structural basis of conformational transitions in the active site and 80 s loop in the…
9LYG 1.26 Å, Crystal structure of FKBP12 complexed with Small Molecule Anchor for Protein-201
2PPO 1.29 Å, Crystal structure of E60A mutant of FKBP12
7U8D 1.39 Å, FKBP12 mutant V55G bound to Rapa*-3Z
9DTW 1.39 Å, Co-crystal structure of the ternary complex of human FKBP12, QDPR and Compound 4

Browse structure collections

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