MolNFT v1 · #139162 · protein
Crystal structure of human heteropentameric complex
5X6U · Ragulator complex protein LAMTOR3: “Crystal structure of human heteropentameric complex”. X-ray diffraction, 6 pockets (best druggability 0.61). MolNFT v1 #139162 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5X6U
- Type
- protein
- Length
- 499 residues
- Chains
- 5
- 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
- 6 · best druggability 0.61
Structure
x-ray diffraction · 5 distinct chains · 39% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ragulator complex protein LAMTOR3 | protein | 124 | 43% helix, 30% strand | Q9UHA4 |
| B | Ragulator complex protein LAMTOR2 | protein | 117 | 41% helix, 32% strand | Q9Y2Q5 |
| C | Ragulator complex protein LAMTOR5 | protein | 91 | 27% helix, 37% strand | O43504 |
| D | Ragulator complex protein LAMTOR4 | protein | 94 | 26% helix, 36% strand | Q0VGL1 |
| E | Ragulator complex protein LAMTOR1 | protein | 73 | 62% helix, 0% strand | Q6IAA8 |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 272 | 0.61 | 0.79 | 29 | empty |
| 2 | 140 | 0.57 | 0.83 | 27 | empty |
| 3 | 273 | 0.56 | 0.77 | 38 | empty |
| 4 | 91 | 0.50 | 0.82 | 15 | empty |
| 5 | 104 | 0.38 | 0.75 | 20 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1297 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 1178 Ų buried · 14 hydrogen bonds · protein-protein
- C–E · 971 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 889 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 794 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5X6U · Crystal structure of human heteropentameric complex · the same entry in another collection · chain E against E, TM-score 1.00
- 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 0.98
- Q9UHA4 · AlphaFold monomer V2.0 prediction for ragulator complex protein LAMTOR3 (Q9UHA4) · a predicted model of the same protein · chain A against A, TM-score 0.97
- O43504 · AlphaFold monomer V2.0 prediction for ragulator complex protein LAMTOR5 (O43504) · a predicted model of the same protein · chain C against A, TM-score 0.96
- 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 0.90
- Q6IAA8 · AlphaFold monomer V2.0 prediction for ragulator complex protein LAMTOR1 (Q6IAA8) · a predicted model of the same protein · chain E against A, TM-score 0.81
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 5X6U · PDBe 5X6U · UniProt Q9UHA4 · UniProt Q9Y2Q5 · UniProt O43504 · UniProt Q0VGL1 · UniProt Q6IAA8
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