6M4U: FKBP-FRB T2098L mutant

Crystal structure of FKBP-FRB T2098L mutant in complex with rapamycin. Determined by X-ray diffraction at 2.2 Å resolution. Released 26 Aug 2020.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,724
Mol. weight: 50.2 kDa
Ligands: RAP, ZN
Released: 26 Aug 2020

Explore 6M4U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6M4U contains 22 α-helices and 16 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: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	1
α-helix	21	1
β-strand	22-31	10	1
β-strand	36-39	4	1
α-helix	40-42	3
β-strand	47-50	4	1
α-helix	58-64	7
β-strand	72-77	6	1
α-helix	79-81	3
β-strand	88	1	2
β-strand	92	1	2
β-strand	98-107	10	1

Chains B and F: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	2023-2035	13
α-helix	2036-2040	5
α-helix	2041	1
α-helix	2044-2060	17
α-helix	2065-2091	27
α-helix	2094-2111	18

Chain E: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	3
α-helix	17-18	2
α-helix	21	1
β-strand	22-31	10	3
β-strand	36-39	4	3
α-helix	40-43	4
β-strand	47-50	4	3
α-helix	58-64	7
α-helix	67-68	2
β-strand	72-77	6	3
α-helix	79-81	3
β-strand	88	1	4
β-strand	92	1	4
β-strand	98-107	10	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Peptidyl-prolyl cis-trans isomerase FKBP1A	A, E	protein	110	Homo sapiens	P62942 (AlphaFold model)
Serine/threonine-protein kinase mTOR	B, F	protein	95	Homo sapiens	P42345 (AlphaFold model)

Sequence of entity 1 (A, E), FASTA

>6M4U_1 Peptidyl-prolyl cis-trans isomerase FKBP1A (chains A, E)
GSMGVQVETISPGDGRTFPKRGQTCVVHYTGMLEDGKKFDSSRDRNKPFKFMLGKQEVIR
GWEEGVAQMSVGQRAKLTISPDYAYGATGHPGIIPPHATLVFDVELLKLE

Sequence of entity 2 (B, F), FASTA

>6M4U_2 Serine/threonine-protein kinase mTOR (chains B, F)
GSILWHEMWHEGLEEASRLYFGERNVKGMFEVLEPLHAMMERGPQTLKETSFNQAYGRDL
MEAQEWCRKYMKSGNVKDLLQAWDLYYHVFRRISK

Ligands and cofactors

ID	Name	Formula	Copies
RAP	Rapamycin immunosuppressant drug	C51 H79 N O13	2
ZN	Zinc ion	Zn	14

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

Primary citation

Rational design and implementation of a chemically inducible heterotrimerization system. Wu, H.D., Kikuchi, M., Dagliyan, O. et al. Nat Methods (2020) 17:928-936. DOI 10.1038/s41592-020-0913-x · 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

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