9PJ1: Synthetic Fab

Crystal structure of a synthetic Fab (4R) in complex with the ternary assembly of FKBP12, Rapamycin, and the FRB domain of mTOR. Determined by X-ray diffraction at 2.05 Å resolution. Released 17 Jun 2026.

Method: X-ray diffraction
Resolution: 2.05 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,466
Mol. weight: 70.96 kDa
Ligands: RAP
Released: 17 Jun 2026

Explore 9PJ1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9PJ1 contains 27 α-helices and 58 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 C: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	1
α-helix	17-18	2
α-helix	21	1
β-strand	22-31	10	1
β-strand	36-39	4	1
α-helix	40-43	4
β-strand	47-50	4	1
α-helix	58-65	8
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

Chain D: 6 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	2-15	14
α-helix	16-20	5
α-helix	21	1
β-strand	23	1	3
α-helix	24-36	13
α-helix	45-71	27
α-helix	74-91	18

Chain H: 8 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	4
β-strand	11-12	2	5
β-strand	18-25	8	4
α-helix	29-31	3
β-strand	32-39	8	6
β-strand	45-52	8	6
β-strand	58-60	3	6
β-strand	65	1	4
β-strand	68-73	6	4
β-strand	78-83	6	4
α-helix	88-90	3
β-strand	92-100	9	6
β-strand	102-103	2	3
β-strand	106-107	2	3
β-strand	115-116	2	6
β-strand	120-122	3	6
β-strand	123-124	2	5
α-helix	127-129	3
β-strand	130	1	7
α-helix	131-132	2
β-strand	133-137	5	8
β-strand	148-158	11	8
β-strand	159	1	7
β-strand	164-167	4	9
α-helix	168-170	3
β-strand	172	1	9
β-strand	176-178	3	8
α-helix	179-181	3
β-strand	182-183	2	8
β-strand	189-198	10	8
α-helix	199-201	3
β-strand	208-213	6	9
α-helix	214-216	3
β-strand	218-223	6	9

Chain L: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	10
β-strand	11-14	4	11
β-strand	20-26	7	10
β-strand	30	1	12
β-strand	32	1	12
β-strand	34-39	6	11
β-strand	46-50	5	11
β-strand	54-55	2	11
α-helix	56	1
β-strand	63-68	6	10
β-strand	71-76	6	10
α-helix	81-83	3
β-strand	86-91	6	11
β-strand	98-99	2	11
β-strand	103-107	5	11
β-strand	112	1	13
α-helix	113-114	2
β-strand	115-119	5	14
α-helix	120-122	3
α-helix	123-126	4
β-strand	130-140	11	14
β-strand	141	1	13
β-strand	146-151	6	15
β-strand	154-155	2	15
α-helix	156	1
β-strand	160-164	5	14
α-helix	165-168	4
β-strand	174-183	10	14
α-helix	184-189	6
β-strand	192-198	7	15
β-strand	206-211	6	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Peptidyl-prolyl cis-trans isomerase FKBP1A	C	protein	108	Homo sapiens	P62942 (AlphaFold model)
Serine/threonine-protein kinase mTOR	D	protein	92	Homo sapiens	P42345 (AlphaFold model)
Heavy chain	H	protein	227	Homo sapiens
Light chain	L	protein	213	Homo sapiens

Sequence of entity 1 (C), FASTA

>9PJ1_1 Peptidyl-prolyl cis-trans isomerase FKBP1A (chains C)
SGVQVETISPGDGRTFPKRGQTCVVHYTGMLEDGKKFDSSRDRNKPFKFMLGKQEVIRGW
EEGVAQMSVGQRAKLTISPDYAYGATGHPGIIPPHATLVFDVELLKLE

Sequence of entity 2 (D), FASTA

>9PJ1_2 Serine/threonine-protein kinase mTOR (chains D)
ILWHEMWHEGLEEASRLYFGERNVKGMFEVLEPLHAMMERGPQTLKETSFNQAYGRDLME
AQEWCRKYMKSGNVKDLTQAWDLYYHVFRRIS

Sequence of entity 3 (H), FASTA

>9PJ1_3 Heavy chain (chains H)
EVQLVESGGGLVQPGGSLRLSCAASGFNIYSSSIHWVRQAPGKGLEWVAYISSSSGSTSY
ADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARQPYEMKGILSWSHGFDYWGQGT
LVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFP
AVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

Sequence of entity 4 (L), FASTA

>9PJ1_4 Light chain (chains L)
DIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPS
RFSGSRSGTDFTLTISSLQPEDFATYYCQQSSSSLITFGQGTKVEIKRTVAAPSVFIFPP
SDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGG

Ligands and cofactors

ID	Name	Formula	Copies
RAP	Rapamycin immunosuppressant drug	C51 H79 N O13	1

Primary citation

Crystal structure of a synthetic Fab (4R) in complex with the ternary assembly of FKBP12, Rapamycin, and the FRB domain of mTOR. O'Leary, K.M., Slezak, T., Kossiakoff, A.A. To be published.

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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