MolNFT v1 · #143788 · protein

Crystal structure of ragulator

6B9X · Ragulator complex protein LAMTOR1: “Crystal structure of ragulator”. X-ray diffraction, 6 pockets (best druggability 0.67). MolNFT v1 #143788 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6B9X
Type: protein
Length: 488 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ragulator complex protein LAMTOR1; Ragulator complex protein LAMTOR2; Ragulator complex…
UniProt: Q6IAA8, Q9Y2Q5, Q9UHA4, Q0VGL1, A0A0C4DGV4
Pockets: 6 · best druggability 0.67

Structure

x-ray diffraction · 5 distinct chains · 37% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ragulator complex protein LAMTOR1	protein	60	52% helix, 2% strand	Q6IAA8
B	Ragulator complex protein LAMTOR2	protein	126	40% helix, 28% strand	Q9Y2Q5
C	Ragulator complex protein LAMTOR3	protein	121	40% helix, 30% strand	Q9UHA4
D	Ragulator complex protein LAMTOR4	protein	90	26% helix, 40% strand	Q0VGL1
E	Hepatitis B virus X interacting protein	protein	91	31% helix, 37% strand	A0A0C4DGV4

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	497	0.67	0.78	46	empty
2	161	0.56	0.81	24	empty
3	125	0.48	0.79	25	empty
4	104	0.35	0.74	16	empty
5	51	0.33	0.78	15	empty

Interfaces

9 interfaces between chains.

B–C · 1333 Å² buried · 27 hydrogen bonds · protein-protein
D–E · 1049 Å² buried · 18 hydrogen bonds · protein-protein
A–E · 980 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 971 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 672 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

6B9X · Crystal structure of Ragulator · the same entry in another collection · chain E against E, TM-score 1.00
Q9UHA4 · AlphaFold monomer V2.0 prediction for ragulator complex protein LAMTOR3 (Q9UHA4) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 0.94
Q0VGL1 · AlphaFold monomer V2.0 prediction for ragulator complex protein LAMTOR4 (Q0VGL1) · a predicted model of the same protein · chain D against A, TM-score 0.94
Q6IAA8 · AlphaFold monomer V2.0 prediction for ragulator complex protein LAMTOR1 (Q6IAA8) · a predicted model of the same protein · chain A against A, TM-score 0.82

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 Q6IAA8
Every structure of UniProt Q9Y2Q5
Every structure of UniProt Q9UHA4
Every structure of UniProt Q0VGL1
Every structure of UniProt A0A0C4DGV4
Elsewhere: RCSB PDB 6B9X · PDBe 6B9X · UniProt Q6IAA8 · UniProt Q9Y2Q5 · UniProt Q9UHA4 · UniProt Q0VGL1 · UniProt A0A0C4DGV4

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