Research workbench

Cryo-EM structure of the flcn-FNIP2-rag-ragulator complex

Analyse Cryo-EM structure of the flcn-FNIP2-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: 6ULG
Type: protein
Length: 2,052 residues
Chains: 9
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Folliculin; Ragulator complex protein LAMTOR3; Ragulator complex protein LAMTOR2…
UniProt: Q8NFG4, Q9UHA4, Q9Y2Q5, O43504, Q0VGL1, Q6IAA8, Q7L523, Q9HB90, Q9P278
Ligands: GDP, GNP, MG
Pockets: 20 · best druggability 0.80

Structure

electron microscopy · 9 distinct chains · 38% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Folliculin	protein	458	39% helix, 16% strand	Q8NFG4
A	Ragulator complex protein LAMTOR3	protein	121	37% helix, 31% strand	Q9UHA4
B	Ragulator complex protein LAMTOR2	protein	125	42% helix, 25% strand	Q9Y2Q5
C	Ragulator complex protein LAMTOR5	protein	91	27% helix, 31% strand	O43504
D	Ragulator complex protein LAMTOR4	protein	85	21% helix, 42% strand	Q0VGL1
E	Ragulator complex protein LAMTOR1	protein	106	55% helix, 1% strand	Q6IAA8
F	RAS-related GTP-binding protein a	protein	273	39% helix, 21% strand	Q7L523
G	RAS-related GTP-binding protein C	protein	310	37% helix, 19% strand	Q9HB90
N	Folliculin-interacting protein 2	protein	483	37% helix, 12% strand	Q9P278

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · chains L, F, N
GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains G, N
MG · Magnesium ion · metal · chains G

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	617	0.80	0.85	82	GDP
2	775	0.78	0.82	64	empty
3	742	0.75	0.80	59	empty
4	455	0.71	0.81	53	GNP, MG
5	98	0.70	0.93	23	empty

Interfaces

20 interfaces between chains.

L–N · 3983 Å² buried · 33 hydrogen bonds · protein-protein
F–G · 1461 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 1375 Å² buried · 20 hydrogen bonds · protein-protein
A–E · 1102 Å² buried · 8 hydrogen bonds · protein-protein
C–E · 985 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent, 1 disulfide (covalent ligand, disulfide).

Compared structures

6ULG · Cryo-EM structure of the FLCN-FNIP2-Rag-Ragulator complex · the same entry in another collection · chain N against N, TM-score 1.00
Q9HB90 · AlphaFold monomer V2.0 prediction for RAS-related GTP-binding protein C (Q9HB90) · a predicted model of the same protein · chain G against A, TM-score 0.97
Q9UHA4 · AlphaFold monomer V2.0 prediction for ragulator complex protein LAMTOR3 (Q9UHA4) · a predicted model of the same protein · chain A against A, TM-score 0.96
Q9Y2Q5 · AlphaFold monomer V2.0 prediction for ragulator complex protein LAMTOR2 (Q9Y2Q5) · a predicted model of the same protein · chain B against A, TM-score 0.95

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 Q8NFG4
Every structure of UniProt Q9UHA4
Every structure of UniProt Q9Y2Q5
Every structure of UniProt O43504
Every structure of UniProt Q0VGL1
Every structure of UniProt Q6IAA8
Every structure of UniProt Q7L523
Every structure of UniProt Q9HB90
Every structure of UniProt Q9P278
Elsewhere: RCSB PDB 6ULG · PDBe 6ULG · UniProt Q8NFG4 · UniProt Q9UHA4 · UniProt Q9Y2Q5 · UniProt O43504 · UniProt Q0VGL1 · UniProt Q6IAA8 · UniProt Q7L523 · UniProt Q9HB90 · UniProt Q9P278

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