5YXH: Rheb-GDP

Structure of Rheb-GDP. Determined by X-ray diffraction at 2.04 Å resolution. Released 28 Feb 2018.

Method: X-ray diffraction
Resolution: 2.04 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,424
Mol. weight: 78.97 kDa
Ligands: GDP, MG
Released: 28 Feb 2018

Explore 5YXH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5YXH contains 17 α-helices and 24 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: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	5-13	9	1
α-helix	19-28	10
β-strand	41-49	9	1
β-strand	52-60	9	1
α-helix	72-74	3
β-strand	80-86	7	1
α-helix	90-105	16
β-strand	114-119	6	1
α-helix	131-141	11
β-strand	144-147	4	1
α-helix	153-170	18

Chain B: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	6-13	8	2
α-helix	19-28	10
β-strand	41-49	9	2
β-strand	52-60	9	2
β-strand	80-86	7	2
α-helix	90-106	17
β-strand	114-119	6	2
α-helix	131-140	10
β-strand	145-147	3	2
α-helix	153-170	18

Chain C: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	5-13	9	3
α-helix	19-28	10
β-strand	41-49	9	3
β-strand	52-60	9	3
β-strand	80-86	7	3
α-helix	90-107	18
β-strand	114-119	6	3
α-helix	131-140	10
β-strand	145-148	4	3
α-helix	153-170	18

Chain D: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	5-13	9	4
α-helix	19-28	10
β-strand	41-49	9	4
β-strand	52-60	9	4
β-strand	80-86	7	4
α-helix	90-106	17
β-strand	114-119	6	4
α-helix	131-141	11
β-strand	145-147	3	4
α-helix	153-170	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
GTP-binding protein Rheb	A, B, C, D	protein	171	Homo sapiens	Q15382 (AlphaFold model)

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

>5YXH_1 GTP-binding protein Rheb (chains A, B, C, D)
SPQSKSRKIAILGYRSVGKSSLTIQFVEGQFVDSYDPTIENTFTKLITVNGQEYHLQLVD
TAGQDEYSIFPQTYSIDINGYILVYSVTSIKSFEVIKVIHGKLLDMVGKVQIPIMLVGNK
KDLHMERVISYEEGKALAESWNAAFLESSAKENQTAVDVFRRIILEAEKLE

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	4
MG	Magnesium ion	Mg	4

Primary citation

A small molecule inhibitor of Rheb selectively targets mTORC1 signaling. Mahoney, S.J., Narayan, S., Molz, L. et al. Nat Commun (2018) 9:548-548. DOI 10.1038/s41467-018-03035-z · PubMed

Other PDB entries of the same protein (UniProt Q15382 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6BSX 1.65 Å, Crystal structure of rheb in complex with compound 1 at 1.65A resolution
3T5G 1.7 Å, Structure of fully modified farnesylated Rheb in complex with PDE6D
1XTQ 2.0 Å, Structure of small GTPase human Rheb in complex with GDP
3SEA 2.0 Å, Structure of Rheb-Y35A mutant in GDP- and GMPPNP-bound forms
7BTD 2.0 Å, Crystal structure of Rheb Y35N mutant bound to GppNHp
7BTC 2.1 Å, Crystal structure of Rheb Y35N mutant bound to GDP
6BT0 2.6 Å, Crystal structure of rheb in complex with compound NR1
7BTA 2.6 Å, Crystal structure of Rheb D60K mutant bound to GDP
1XTR 2.65 Å, Structure of small GTPase human Rheb in complex with GppNHp
1XTS 2.8 Å, Structure of small GTPase human Rheb in complex with GTP
9ED7 3.16 Å, Active state of mTOR on membrane
9ED4 3.23 Å, A composite map of mTORC1-Rag-Ragultor-4EBP1 on membrane

Browse structure collections

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