MolNFT v1 · #140729 · protein

Human ragulator complex

5YK3 · Ragulator complex protein LAMTOR3: “Human ragulator complex”. X-ray diffraction, 20 pockets (best druggability 0.71). MolNFT v1 #140729 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5YK3
Type: protein
Length: 1,549 residues
Chains: 15
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ragulator complex protein LAMTOR3; Ragulator complex protein LAMTOR2; Ragulator complex…
UniProt: Q9UHA4, Q9Y2Q5, O43504, Q0VGL1, Q6IAA8
Pockets: 20 · best druggability 0.71

Structure

x-ray diffraction · 12 distinct chains · 35% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
m, H	Ragulator complex protein LAMTOR3	protein	124	41% helix, 30% strand	Q9UHA4
l	Ragulator complex protein LAMTOR2	protein	124	36% helix, 30% strand	Q9Y2Q5
o	Ragulator complex protein LAMTOR5	protein	90	29% helix, 38% strand	O43504
n	Ragulator complex protein LAMTOR4	protein	88	23% helix, 35% strand	Q0VGL1
k	Ragulator complex protein LAMTOR1	protein	85	51% helix, 1% strand	Q6IAA8
C	Ragulator complex protein LAMTOR3	protein	123	40% helix, 30% strand	Q9UHA4
B	Ragulator complex protein LAMTOR2	protein	125	31% helix, 28% strand	Q9Y2Q5
E, J	Ragulator complex protein LAMTOR5	protein	91	30% helix, 37% strand	O43504
D	Ragulator complex protein LAMTOR4	protein	96	26% helix, 33% strand	Q0VGL1
A, F	Ragulator complex protein LAMTOR1	protein	85	53% helix, 0% strand	Q6IAA8
G	Ragulator complex protein LAMTOR2	protein	123	35% helix, 28% strand	Q9Y2Q5
I	Ragulator complex protein LAMTOR4	protein	95	22% helix, 38% strand	Q0VGL1

Pockets

20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	580	0.71	0.79	68	empty
2	542	0.69	0.79	55	empty
3	459	0.68	0.80	61	empty
4	344	0.61	0.77	43	empty
5	173	0.58	0.82	27	empty

Interfaces

36 interfaces between chains.

C–B · 1316 Å² buried · 21 hydrogen bonds · protein-protein
H–G · 1277 Å² buried · 22 hydrogen bonds · protein-protein
m–l · 1264 Å² buried · 23 hydrogen bonds · protein-protein
D–A · 1068 Å² buried · 7 hydrogen bonds · protein-protein
H–F · 1052 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

5YK3 · human Ragulator complex · the same entry in another collection · chain A against A, 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 Q9UHA4
Every structure of UniProt Q9Y2Q5
Every structure of UniProt O43504
Every structure of UniProt Q0VGL1
Every structure of UniProt Q6IAA8
Elsewhere: RCSB PDB 5YK3 · PDBe 5YK3 · UniProt Q9UHA4 · UniProt Q9Y2Q5 · UniProt O43504 · UniProt Q0VGL1 · UniProt Q6IAA8

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