Research workbench

GATOR1-rag-ragulator - inhibitory complex

Analyse GATOR1-rag-ragulator - inhibitory complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7T3A
Type: protein
Length: 2,897 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gator complex protein DEPDC5; Gator complex protein NPRL2; Gator complex protein NPRL3…
UniProt: O75140, Q8WTW4, Q12980, Q7L523, Q9HB90, Q6IAA8, Q9Y2Q5, Q9UHA4, Q0VGL1, O43504
Ligands: GNP
Pockets: 20 · best druggability 0.81

Structure

electron microscopy · 10 distinct chains · 33% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Gator complex protein DEPDC5	protein	990	26% helix, 24% strand	O75140
B	Gator complex protein NPRL2	protein	362	31% helix, 16% strand	Q8WTW4
C	Gator complex protein NPRL3	protein	406	43% helix, 16% strand	Q12980
K	RAS-related GTP-binding protein a	protein	294	42% helix, 23% strand	Q7L523
L	RAS-related GTP-binding protein C	protein	299	36% helix, 12% strand	Q9HB90
M	Ragulator complex protein LAMTOR1	protein	115	46% helix, 1% strand	Q6IAA8
N	Ragulator complex protein LAMTOR2	protein	125	35% helix, 23% strand	Q9Y2Q5
O	Ragulator complex protein LAMTOR3	protein	118	38% helix, 29% strand	Q9UHA4
P	Ragulator complex protein LAMTOR4	protein	97	18% helix, 35% strand	Q0VGL1
Q	Ragulator complex protein LAMTOR5	protein	91	25% helix, 32% strand	O43504

Ligands and binding sites

GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains K

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	200	0.81	0.95	29	empty
2	497	0.80	0.86	60	empty
3	1184	0.80	0.81	125	empty
4	616	0.78	0.84	53	empty
5	1020	0.78	0.80	109	empty

Interfaces

20 interfaces between chains.

B–C · 1843 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 1775 Å² buried · 12 hydrogen bonds · protein-protein
K–L · 1620 Å² buried · 12 hydrogen bonds · protein-protein
N–O · 1378 Å² buried · 24 hydrogen bonds · protein-protein
P–Q · 1172 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent, 1 disulfide (covalent ligand, disulfide).

Compared structures

7T3A · GATOR1-RAG-RAGULATOR - Inhibitory Complex · the same entry in another collection · chain Q against Q, TM-score 1.00
O75140 · AlphaFold monomer V2.0 prediction for gator complex protein DEPDC5 (O75140) · a predicted model of the same protein · chain A against A, TM-score 0.98
Q7L523 · AlphaFold monomer V2.0 prediction for RAS-related GTP-binding protein a (Q7L523) · a predicted model of the same protein · chain K against A, TM-score 0.97

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 O75140
Every structure of UniProt Q8WTW4
Every structure of UniProt Q12980
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 7T3A · PDBe 7T3A · UniProt O75140 · UniProt Q8WTW4 · UniProt Q12980 · UniProt Q7L523 · UniProt Q9HB90 · UniProt Q6IAA8 · UniProt Q9Y2Q5 · UniProt Q9UHA4 · UniProt Q0VGL1 · UniProt O43504

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