Research workbench

GATOR1-rag-ragulator - gap complex

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

PDB: 7T3B
Type: protein
Length: 2,892 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RAS-related GTP-binding protein C; Gator complex protein NPRL2; Gator complex protein…
EC: 3.6.5.-
UniProt: Q9HB90, Q8WTW4, O75140, Q9UHA4, Q9Y2Q5, O43504, Q0VGL1, Q6IAA8, Q12980, Q7L523
Ligands: GDP, AF3
Pockets: 20 · best druggability 0.80

Structure

electron microscopy · 10 distinct chains · 35% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E	RAS-related GTP-binding protein C (EC 3.6.5.-)	protein	305	39% helix, 14% strand	Q9HB90
B	Gator complex protein NPRL2	protein	362	38% helix, 16% strand	Q8WTW4
A	Gator complex protein DEPDC5	protein	989	26% helix, 23% strand	O75140
H	Ragulator complex protein LAMTOR3	protein	120	37% helix, 29% strand	Q9UHA4
G	Ragulator complex protein LAMTOR2	protein	124	41% helix, 27% strand	Q9Y2Q5
J	Ragulator complex protein LAMTOR5	protein	91	26% helix, 35% strand	O43504
I	Ragulator complex protein LAMTOR4	protein	89	20% helix, 30% strand	Q0VGL1
F	Ragulator complex protein LAMTOR1	protein	111	50% helix, 0% strand	Q6IAA8
C	Gator complex protein NPRL3	protein	405	45% helix, 18% strand	Q12980
D	RAS-related GTP-binding protein a	protein	296	40% helix, 22% strand	Q7L523

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains E, B, D
AF3 · Aluminum fluoride · ligand · 2 copies · chains E, B, D

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	176	0.80	0.96	31	empty
2	799	0.78	0.82	88	empty
3	482	0.75	0.83	69	GDP
4	688	0.74	0.80	69	empty
5	921	0.74	0.78	99	empty

Interfaces

21 interfaces between chains.

B–C · 2009 Å² buried · 18 hydrogen bonds · protein-protein
B–A · 1903 Å² buried · 6 hydrogen bonds · protein-protein
E–D · 1562 Å² buried · 20 hydrogen bonds · protein-protein
H–G · 1397 Å² buried · 25 hydrogen bonds · protein-protein
H–F · 1142 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

7T3B · GATOR1-RAG-RAGULATOR - GAP Complex · the same entry in another collection · chain D against D, 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 D 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 Q9HB90
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
Elsewhere: RCSB PDB 7T3B · PDBe 7T3B · UniProt Q9HB90 · UniProt Q8WTW4 · UniProt O75140 · UniProt Q9UHA4 · UniProt Q9Y2Q5 · UniProt O43504 · UniProt Q0VGL1 · UniProt Q6IAA8 · UniProt Q12980 · UniProt Q7L523

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