9DBO: Synthetic Fab

Crystal structure of a synthetic Fab (R3E9) in complex with the FRB domain of mTOR. Determined by X-ray diffraction at 1.55 Å resolution. Released 11 Jun 2025.

Method: X-ray diffraction
Resolution: 1.55 Å
Organism: Homo sapiens
Chains: 3
Atoms: 4,647
Mol. weight: 58.27 kDa
Released: 11 Jun 2025

Explore 9DBO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9DBO contains 23 α-helices and 48 β-strands across 3 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 C: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	2023-2035	13
α-helix	2036-2040	5
α-helix	2041	1
α-helix	2044-2059	16
α-helix	2065-2091	27
α-helix	2094-2112	19

Chain H: 10 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	1
β-strand	13-15	3	2
β-strand	21-28	8	1
α-helix	32-34	3
β-strand	36-42	7	2
β-strand	48-55	8	2
β-strand	60-63	4	2
β-strand	71-76	6	1
α-helix	77-79	3
β-strand	81-86	6	1
α-helix	91-93	3
β-strand	95-106	12	2
β-strand	110-116	7	2
β-strand	120-124	5	2
α-helix	128-129	2
β-strand	130	1	3
α-helix	131-132	2
β-strand	133-137	5	4
α-helix	141-143	3
β-strand	144-145	2	4
β-strand	148-158	11	4
β-strand	159	1	3
β-strand	164-167	4	5
α-helix	168-170	3
β-strand	172	1	5
β-strand	176-178	3	4
α-helix	179-181	3
β-strand	182-183	2	4
β-strand	189-198	10	4
α-helix	199-201	3
β-strand	202	1	6
β-strand	205	1	6
β-strand	208-213	6	5
α-helix	214-216	3
β-strand	218-223	6	5

Chain L: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	7
β-strand	11-14	4	8
β-strand	20-26	7	7
β-strand	30	1	9
β-strand	32	1	9
β-strand	34-39	6	8
β-strand	46-50	5	8
β-strand	54-55	2	8
α-helix	56	1
β-strand	63-68	6	7
β-strand	71-76	6	7
α-helix	81-83	3
β-strand	86-91	6	8
β-strand	98-99	2	8
β-strand	103-107	5	8
β-strand	112	1	10
α-helix	113-114	2
β-strand	115-119	5	11
α-helix	120-122	3
α-helix	123-128	6
β-strand	130-140	11	11
β-strand	141	1	10
β-strand	146-151	6	12
β-strand	154-155	2	12
β-strand	160-164	5	11
α-helix	165-168	4
β-strand	174-183	10	11
α-helix	184-187	4
β-strand	192-198	7	12
β-strand	206-211	6	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine/threonine-protein kinase mTOR	C	protein	93	Homo sapiens	P42345 (AlphaFold model)
Fab heavy chain	H	protein	224	Homo sapiens
Fab light chain	L	protein	212	Homo sapiens

Sequence of entity 1 (C), FASTA

>9DBO_1 Serine/threonine-protein kinase mTOR (chains C)
ILWHEMWHEGLEEASRLYFGERNVKGMFEVLEPLHAMMERGPQTLKETSFNQAYGRDLME
AQEWCRKYMKSGNVKDLTQAWDLYYHVFRRISK

Sequence of entity 2 (H), FASTA

>9DBO_2 Fab heavy chain (chains H)
EVQLVESGGGLVQPGGSLRLSCAASGFNVYSYSIHWVRQAPGKGLEWVASIYPSSGYTSY
ADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARGTYYFYFMSWGLDYWGQGTLVT
VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL
QSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

Sequence of entity 3 (L), FASTA

>9DBO_3 Fab light chain (chains L)
DIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPS
RFSGSRSGTDFTLTISSLQPEDFATYYCQQYFSSLFTFGQGTKVEIKRTVAAPSVFIFPP
SDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRG

Primary citation

Conformation-specific synthetic intrabodies modulate mTOR signaling with subcellular spatial resolution. O'Leary, K.M., Slezak, T., Kossiakoff, A.A. Proc Natl Acad Sci U S A (2025) 122:e2424679122-e2424679122. DOI 10.1073/pnas.2424679122 · PubMed

Other PDB entries of the same protein (UniProt P42345 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4DRI 1.45 Å, Co-crystal structure of the PPIase domain of FKBP51, Rapamycin and the FRB fragment of…
5GPG 1.67 Å, Co-crystal structure of the FK506 binding domain of human FKBP25, Rapamycin and the FRB…
5WBH 1.75 Å, Structure of the FRB domain of mTOR bound to a substrate recruitment peptide of S6K1
4DRJ 1.8 Å, o-crystal structure of the PPIase domain of FKBP52, Rapamycin and the FRB fragment of mTOR
3FAP 1.85 Å, Atomic structures of the rapamycin analogs in complex with both human FKBP12 and frb…
8PPZ 1.85 Å, Co-crystal structure of FKBP12, compound 7 and the FRB fragment of mTOR
8XI9 1.85 Å, Crystal structure of FRB-FKBP fusion protein in complex with rapamycin
9PIW 1.9 Å, Crystal structure of a synthetic Fab (1A) in complex with the FRB domain of mTOR
9DL0 2.0 Å, Crystal structure of a synthetic Fab (R3H8) in complex with the FRB domain of mTOR
9PJ1 2.05 Å, Crystal structure of a synthetic Fab (4R) in complex with the ternary assembly of…
9PIU 2.18 Å, Crystal structure of a synthetic Fab (2C) in complex with the FRB domain of mTOR
1NSG 2.2 Å, The structure of the immunophilin-immunosuppressant FKBP12-rapamycin complex interacting…

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