MolNFT v1 · #187927 · protein

GATOR1-rag-ragulator - dual complex

7T3C · Gator complex protein NPRL2: “GATOR1-rag-ragulator - dual complex”. Electron microscopy, 2 ligands (GDP, AF3), 20 pockets (best druggability 0.77). MolNFT v1 #187927 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7T3C
Type: protein
Length: 4,047 residues
Chains: 17
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gator complex protein NPRL2; Gator complex protein DEPDC5; Ragulator complex protein…
EC: 3.6.5.-
UniProt: Q8WTW4, O75140, Q9UHA4, Q9Y2Q5, O43504, Q0VGL1, Q6IAA8, Q12980, Q7L523, Q9HB90
Ligands: GDP, AF3
Pockets: 20 · best druggability 0.77

Structure

electron microscopy · 16 distinct chains · 35% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Gator complex protein NPRL2	protein	362	36% helix, 17% strand	Q8WTW4
A	Gator complex protein DEPDC5	protein	990	25% helix, 23% strand	O75140
H	Ragulator complex protein LAMTOR3	protein	121	39% helix, 27% strand	Q9UHA4
G	Ragulator complex protein LAMTOR2	protein	125	40% helix, 24% strand	Q9Y2Q5
J, Q	Ragulator complex protein LAMTOR5	protein	91	26% helix, 26% strand	O43504
I	Ragulator complex protein LAMTOR4	protein	85	18% helix, 32% strand	Q0VGL1
F	Ragulator complex protein LAMTOR1	protein	111	50% helix, 1% strand	Q6IAA8
C	Gator complex protein NPRL3	protein	406	44% helix, 15% strand	Q12980
D	RAS-related GTP-binding protein a	protein	296	40% helix, 21% strand	Q7L523
E	RAS-related GTP-binding protein C (EC 3.6.5.-)	protein	306	40% helix, 14% strand	Q9HB90
O	Ragulator complex protein LAMTOR3	protein	120	37% helix, 29% strand	Q9UHA4
N	Ragulator complex protein LAMTOR2	protein	124	30% helix, 25% strand	Q9Y2Q5
P	Ragulator complex protein LAMTOR4	protein	97	22% helix, 35% strand	Q0VGL1
M	Ragulator complex protein LAMTOR1	protein	115	43% helix, 0% strand	Q6IAA8
K	RAS-related GTP-binding protein a	protein	300	40% helix, 23% strand	Q7L523
L	RAS-related GTP-binding protein C	protein	307	39% helix, 14% strand	Q9HB90

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 3 copies · chains B, D, E, K
AF3 · Aluminum fluoride · ligand · 3 copies · chains B, D, E, 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	116	0.77	0.96	26	empty
2	409	0.77	0.87	56	empty
3	719	0.77	0.82	92	empty
4	577	0.77	0.83	82	empty
5	512	0.76	0.84	51	empty

Interfaces

40 interfaces between chains.

B–C · 2044 Å² buried · 17 hydrogen bonds · protein-protein
B–A · 1700 Å² buried · 4 hydrogen bonds · protein-protein
K–L · 1430 Å² buried · 18 hydrogen bonds · protein-protein
D–E · 1395 Å² buried · 26 hydrogen bonds · protein-protein
O–N · 1356 Å² buried · 30 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

7T3C · GATOR1-RAG-RAGULATOR - Dual Complex · the same entry in another collection · chain O against O, TM-score 1.00

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 Q8WTW4
Every structure of UniProt O75140
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 Q12980
Every structure of UniProt Q7L523
Every structure of UniProt Q9HB90
Elsewhere: RCSB PDB 7T3C · PDBe 7T3C · UniProt Q8WTW4 · UniProt O75140 · UniProt Q9UHA4 · UniProt Q9Y2Q5 · UniProt O43504 · UniProt Q0VGL1 · UniProt Q6IAA8 · UniProt Q12980 · UniProt Q7L523 · UniProt Q9HB90

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