8PPZ: Peptidyl-prolyl cis-trans isomerase FKBP1A

Name: PDB 8PPZ: Co-crystal structure of FKBP12, compound 7 and the FRB fragment of mTOR
Published: 2023-08-09
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: isomerase

Co-crystal structure of FKBP12, compound 7 and the FRB fragment of mTOR. Determined by X-ray diffraction at 1.85 Å resolution. Released 9 Aug 2023.

Method: X-ray diffraction
Resolution: 1.85 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,766
Mol. weight: 24.39 kDa
Ligands: CA, 0AN
Released: 9 Aug 2023

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

Secondary structure: helices and β-sheets

8PPZ contains 10 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: 3 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	57-63	7
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: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	2021-2035	15
α-helix	2036-2040	5
α-helix	2044-2059	16
α-helix	2065-2070	6
α-helix	2071-2075	5
α-helix	2076-2091	16
α-helix	2094-2110	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Peptidyl-prolyl cis-trans isomerase FKBP1A	A	protein	107	Homo sapiens	P62942 (AlphaFold model)
Serine/threonine-protein kinase mTOR	B	protein	98	Homo sapiens	P42345 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8PPZ_1 Peptidyl-prolyl cis-trans isomerase FKBP1A (chains A)
GVQVETISPGDGRTFPKRGQTVVVHYTGMLEDGKKFDSSRDRNKPFKFMLGKQEVIRGWE
EGVAQMSVGQRAKLTISPDYAYGATGHPGIIPPHATLVFDVELLKLE

Sequence of entity 2 (B), FASTA

>8PPZ_2 Serine/threonine-protein kinase mTOR (chains B)
GAMDPEFMEMWHEGLEEASRLYFGERNVKGMFEVLEPLHAMMERGPQTLKETSFNQAYGR
DLMEAQEWCRKYMKSGNVKDLTQAWDLYYHVFRRISKQ

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	4
0AN	(1~{S},5~{S},6~{R})-10-[3,5-bis(chloranyl)phenyl]sulfonyl-5-[(~{E})-2-(2-chloro…	C28 H26 Cl3 N3 O3 S	1

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

Primary citation

Co-crystal structure of FKBP12, compound 7 and the FRB fragment of mTOR. Meyners, C., Deutscher, R.C.E., Hausch, F. ChemRxiv (2023). DOI 10.26434/chemrxiv-2023-4vb0m

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

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