3FAP: Atomic structures of the rapamycin analogs

Atomic structures of the rapamycin analogs in complex with both human FKBP12 and frb domain of frap. Determined by X-ray diffraction at 1.85 Å resolution. Released 13 Sept 2000.

Method: X-ray diffraction
Resolution: 1.85 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,890
Mol. weight: 24.15 kDa
Ligands: ARD
Released: 13 Sept 2000

Explore 3FAP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3FAP contains 9 α-helices and 8 β-strands across 2 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: 4 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
α-helix	40-42	3
β-strand	46-49	4	1
α-helix	57-64	8
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

Chain B: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	112-124	13
α-helix	125-129	5
α-helix	133-149	17
α-helix	154-180	27
α-helix	183-200	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
FK506-binding protein	A	protein	107	Homo sapiens	P62942 (AlphaFold model)
FKBP12-rapamycin associated protein	B	protein	94	Homo sapiens	P42345 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3FAP_1 FK506-BINDING PROTEIN (chains A)
GVQVETISPGDGRTFPKRGQTCVVHYTGMLEDGKKFDSSRDRNKPFKFMLGKQEVIRGWE
EGVAQMSVGQRAKLTISPDYAYGATGHPGIIPPHATLVFDVELLKLE

Sequence of entity 2 (B), FASTA

>3FAP_2 FKBP12-RAPAMYCIN ASSOCIATED PROTEIN (chains B)
VAILWHEMWHEGLEEASRLYFGERNVKGMFEVLEPLHAMMERGPQTLKETSFNQAYGRDL
MEAQEWCRKYMKSGNVKDLTQAWDLYYHVFRRIS

Ligands and cofactors

ID	Name	Formula	Copies
ARD	C15-(R)-methylthienyl rapamycin	C55 H81 N O12 S	1

Primary citation

Refined structure of the FKBP12-rapamycin-FRB ternary complex at 2.2 A resolution. Liang, J., Choi, J., Clardy, J. Acta Crystallogr D Biol Crystallogr (1999) 55:736-744. DOI 10.1107/S0907444998014747 · 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…
8PDF 1.2 Å, FKBP12 in complex with PROTAC 6a2
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

Browse structure collections

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