9PDM: Leucine-bound Sestrin2 from Homo sapiens

Leucine-bound Sestrin2 from Homo sapiens (GATOR2-inspired update). Determined by X-ray diffraction at 2.7 Å resolution. Released 12 Aug 2026.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 5
Atoms: 15,999
Mol. weight: 273.46 kDa
Ligands: LEU
Released: 12 Aug 2026

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

Secondary structure: helices and β-sheets

9PDM contains 139 α-helices and 30 β-strands across 5 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: 28 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	45	1	1
α-helix	50-54	5
α-helix	68-73	6
α-helix	78-83	6
α-helix	87-102	16
α-helix	109-121	13
α-helix	126-138	13
α-helix	143-147	5
α-helix	149-151	3
α-helix	154-157	4
α-helix	160-168	9
α-helix	170-172	3
α-helix	175-182	8
α-helix	191-213	23
β-strand	216	1	1
α-helix	217-219	3
α-helix	256-271	16
α-helix	283-292	10
α-helix	310-315	6
α-helix	334-336	3
β-strand	337-338	2	2
α-helix	339-341	3
α-helix	344-348	5
α-helix	349-355	7
α-helix	357-372	16
β-strand	377-378	2	3
β-strand	381-382	2	3
α-helix	387-400	14
β-strand	403-404	2	2
α-helix	411-416	6
α-helix	419-430	12
α-helix	432-434	3
α-helix	437-442	6
α-helix	449-479	31

Chain B: 28 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	45	1	4
α-helix	50-54	5
α-helix	68-71	4
α-helix	78-83	6
α-helix	87-102	16
α-helix	109-121	13
α-helix	126-138	13
α-helix	143-147	5
α-helix	149-151	3
α-helix	154-157	4
α-helix	160-168	9
α-helix	170-172	3
α-helix	175-182	8
α-helix	191-213	23
β-strand	216	1	4
α-helix	217-219	3
α-helix	256-272	17
α-helix	280-292	13
α-helix	311-315	5
α-helix	334-336	3
β-strand	337-338	2	5
α-helix	339-341	3
α-helix	344-348	5
α-helix	349-355	7
α-helix	357-372	16
β-strand	377-378	2	6
β-strand	381-382	2	6
α-helix	387-400	14
β-strand	403-404	2	5
α-helix	411-416	6
α-helix	419-430	12
α-helix	432-434	3
α-helix	437-442	6
α-helix	449-478	30

Chain C: 28 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	45	1	7
α-helix	50-54	5
α-helix	68-73	6
α-helix	78-83	6
α-helix	87-102	16
α-helix	109-121	13
α-helix	126-138	13
α-helix	143-147	5
α-helix	149-151	3
α-helix	154-157	4
α-helix	160-168	9
α-helix	170-172	3
α-helix	175-182	8
α-helix	191-213	23
β-strand	216	1	7
α-helix	217-219	3
α-helix	256-274	19
α-helix	280-292	13
α-helix	312-315	4
α-helix	334-336	3
β-strand	337-338	2	8
α-helix	339-341	3
α-helix	344-348	5
α-helix	349-355	7
α-helix	357-372	16
β-strand	377-378	2	9
β-strand	381-382	2	9
α-helix	387-400	14
β-strand	403-404	2	8
α-helix	411-416	6
α-helix	419-430	12
α-helix	432-434	3
α-helix	437-442	6
α-helix	449-479	31

Chain D: 27 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	45	1	10
α-helix	68-71	4
α-helix	78-83	6
α-helix	87-102	16
α-helix	109-121	13
α-helix	126-138	13
α-helix	143-147	5
α-helix	149-151	3
α-helix	154-157	4
α-helix	160-168	9
α-helix	170-172	3
α-helix	175-182	8
α-helix	191-213	23
β-strand	216	1	10
α-helix	217-219	3
α-helix	256-271	16
α-helix	280-292	13
α-helix	311-315	5
α-helix	334-336	3
β-strand	337-338	2	11
α-helix	339-341	3
α-helix	344-348	5
α-helix	349-355	7
α-helix	357-372	16
β-strand	377-378	2	12
β-strand	381-382	2	12
α-helix	387-400	14
β-strand	403-404	2	11
α-helix	411-416	6
α-helix	419-430	12
α-helix	432-434	3
α-helix	437-442	6
α-helix	449-479	31

Chain E: 28 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	45	1	13
α-helix	50-54	5
α-helix	68-71	4
α-helix	78-83	6
α-helix	87-102	16
α-helix	109-121	13
α-helix	126-138	13
α-helix	143-147	5
α-helix	149-151	3
α-helix	154-158	5
α-helix	160-168	9
α-helix	170-172	3
α-helix	175-182	8
α-helix	191-213	23
β-strand	216	1	13
α-helix	217-219	3
α-helix	256-273	18
α-helix	280-292	13
α-helix	310-315	6
α-helix	334-336	3
β-strand	337-338	2	14
α-helix	339-341	3
α-helix	344-348	5
α-helix	349-355	7
α-helix	357-372	16
β-strand	377-378	2	15
β-strand	381-382	2	15
α-helix	387-400	14
β-strand	403-404	2	14
α-helix	411-416	6
α-helix	419-430	12
α-helix	432-434	3
α-helix	437-442	6
α-helix	449-479	31

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sestrin-2	A, B, C, D, E	protein	480	Homo sapiens	P58004 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E), FASTA

>9PDM_1 Sestrin-2 (chains A, B, C, D, E)
MIVADSECRAELKDYLRFAPGGVGDSGPGEEQRESRARRGPRGPSAFIPVEEVLREGAES
LEQHLGLEALMSSGRVDNLAVVMGLHPDYFTSFWRLHYLLLHTDGPLASSWRHYIAIMAA
ARHQCSYLVGSHMAEFLQTGGDPEWLLGLHRAPEKLRKLSEINKLLAHRPWLITKEHIQA
LLKTGEHTWSLAELIQALVLLTHCHSLSSFVFGCGILPEGDADGSPAPQAPTPPSEQSSP
PSRDPLNNSGGFESARDVEALMERMQQLQESLLRDEGTSQEEMESRFELEKSESLLVTPS
ADILEPSPHPDMLCFVEDPTFGYEDFTRRGAQAPPTFRAQDYTWEDHGYSLIQRLYPEGG
QLLDEKFQAAYSLTYNTIAMHSGVDTSVLRRAIWNYIHCVFGIRYDDYDYGEVNQLLERN
LKVYIKTVACYPEKTTRRMYNLFWRHFRHSEKVHVNLLLLEARMQAALLYALRAITRYMT

Ligands and cofactors

ID	Name	Formula	Copies
LEU	Leucine	C6 H13 N O2	5

Primary citation

Structural basis for the dynamic regulation of mTORC1 by amino acids. Valenstein, M.L., Wranik, M., Lalgudi, P.V. et al. Nature (2025) 646:493-500. DOI 10.1038/s41586-025-09428-7 · PubMed

Other PDB entries of the same protein (UniProt P58004 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5DJ4 2.7 Å, Leucine-bound Sestrin2 from Homo sapiens
5T0N 3.0 Å, Pseudo-apo structure of Sestrin2 at 3.0 angstrom resolution
6N0M 3.3 Å, Crystal structure of SESTRIN2 in complex with nv-0005138
9DX1 3.36 Å, Human GATOR2 complex - Sestrin2 bound state
9LWF 3.41 Å, Cryo-EM structure of dual sensor bound GATOR2 complex
5CUF 3.5 Å, X-ray crystal structure of SeMet human Sestrin2
9LVJ 3.82 Å, Cryo-EM structure of Sestrin2 bound human GATOR2 complex

Browse structure collections

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