MolNFT v1 · #141141 · protein

Structure of rheb-GDP

5YXH · GTP-binding protein rheb: “Structure of rheb-GDP”. X-ray diffraction, 2 ligands (GDP, MG), 10 pockets (best druggability 0.75). MolNFT v1 #141141 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5YXH
Type: protein
Length: 651 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GTP-binding protein rheb
UniProt: Q15382
Ligands: GDP, MG
Pockets: 10 · best druggability 0.75

Structure

x-ray diffraction · 4 distinct chains · 35% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	GTP-binding protein rheb	protein	165	35% helix, 27% strand	Q15382
B	GTP-binding protein rheb	protein	164	34% helix, 26% strand	Q15382
C	GTP-binding protein rheb	protein	157	36% helix, 28% strand	Q15382
D	GTP-binding protein rheb	protein	165	34% helix, 26% strand	Q15382

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1137	0.75	0.77	140	empty
2	162	0.46	0.76	27	empty
3	123	0.45	0.78	23	GDP, MG
4	112	0.45	0.79	24	GDP, MG
5	144	0.45	0.76	26	empty

Interfaces

5 interfaces between chains.

B–C · 437 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 430 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 417 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 152 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 149 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5YXH · Structure of Rheb-GDP · the same entry in another collection · chain D against D, TM-score 1.00
Q15382 · AlphaFold monomer V2.0 prediction for GTP-binding protein rheb (Q15382) · a predicted model of the same protein · chain A against A, TM-score 0.98

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q15382
Elsewhere: RCSB PDB 5YXH · PDBe 5YXH · UniProt Q15382

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