Research workbench

Raptor-rag-ragulator complex

Analyse Raptor-rag-ragulator complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6U62
Type: protein
Length: 2,214 residues
Chains: 8
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Regulatory-associated protein of mtor; RAS-related GTP-binding protein a; RAS-related…
UniProt: Q8N122, Q7L523, Q9HB90, Q6IAA8, Q9Y2Q5, Q9UHA4, Q0VGL1, O43504
Ligands: GTP, GDP, MG
Pockets: 20 · best druggability 0.81

Structure

electron microscopy · 8 distinct chains · 38% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Regulatory-associated protein of mtor	protein	1110	38% helix, 16% strand	Q8N122
B	RAS-related GTP-binding protein a	protein	298	39% helix, 26% strand	Q7L523
C	RAS-related GTP-binding protein C	protein	281	42% helix, 20% strand	Q9HB90
D	Ragulator complex protein LAMTOR1	protein	108	50% helix, 1% strand	Q6IAA8
E	Ragulator complex protein LAMTOR2	protein	124	42% helix, 27% strand	Q9Y2Q5
F	Ragulator complex protein LAMTOR3	protein	120	38% helix, 23% strand	Q9UHA4
G	Ragulator complex protein LAMTOR4	protein	84	15% helix, 24% strand	Q0VGL1
H	Ragulator complex protein LAMTOR5	protein	89	25% helix, 31% strand	O43504

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · chains B
GDP · Guanosine-5'-diphosphate · ligand · chains A, C
MG · Magnesium ion · metal · chains B

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

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1140	0.81	0.83	69	empty
2	774	0.77	0.81	97	empty
3	712	0.77	0.81	60	empty
4	407	0.76	0.85	39	empty
5	612	0.76	0.82	57	empty

Interfaces

17 interfaces between chains.

A–B · 1534 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 1400 Å² buried · 21 hydrogen bonds · protein-protein
E–F · 1269 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 1058 Å² buried · 11 hydrogen bonds · protein-protein
D–E · 805 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

6U62 · Raptor-Rag-Ragulator complex · the same entry in another collection · chain H against H, TM-score 1.00
Q7L523 · AlphaFold monomer V2.0 prediction for RAS-related GTP-binding protein a (Q7L523) · a predicted model of the same protein · chain B against A, TM-score 0.98
Q9UHA4 · AlphaFold monomer V2.0 prediction for ragulator complex protein LAMTOR3 (Q9UHA4) · a predicted model of the same protein · chain F against A, TM-score 0.96
Q8N122 · AlphaFold monomer V2.0 prediction for regulatory-associated protein of mtor (Q8N122) · a predicted model of the same protein · chain A against A, TM-score 0.96
Q9HB90 · AlphaFold monomer V2.0 prediction for RAS-related GTP-binding protein C (Q9HB90) · a predicted model of the same protein · chain C against A, TM-score 0.94

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 Q8N122
Every structure of UniProt Q7L523
Every structure of UniProt Q9HB90
Every structure of UniProt Q6IAA8
Every structure of UniProt Q9Y2Q5
Every structure of UniProt Q9UHA4
Every structure of UniProt Q0VGL1
Every structure of UniProt O43504
Elsewhere: RCSB PDB 6U62 · PDBe 6U62 · UniProt Q8N122 · UniProt Q7L523 · UniProt Q9HB90 · UniProt Q6IAA8 · UniProt Q9Y2Q5 · UniProt Q9UHA4 · UniProt Q0VGL1 · UniProt O43504

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