Research workbench
The crystal structure of the human lamtor complex
Analyse The crystal structure of the human lamtor complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EHP
- Type
- protein
- Length
- 490 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
- Ligands
- CL
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 5 distinct chains · 36% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ragulator complex protein LAMTOR3 | protein | 122 | 37% helix, 31% strand | Q9UHA4 |
| B | Ragulator complex protein LAMTOR2 | protein | 115 | 39% helix, 32% strand | Q9Y2Q5 |
| C | Ragulator complex protein LAMTOR5 | protein | 91 | 29% helix, 38% strand | O43504 |
| D | Ragulator complex protein LAMTOR4 | protein | 92 | 24% helix, 39% strand | Q0VGL1 |
| E | Ragulator complex protein LAMTOR1 | protein | 70 | 57% helix, 0% strand | Q6IAA8 |
Ligands and binding sites
- CL · Chloride ion · ion · chains D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 469 | 0.68 | 0.79 | 45 | empty |
| 2 | 352 | 0.66 | 0.80 | 56 | empty |
| 3 | 92 | 0.33 | 0.73 | 13 | empty |
| 4 | 75 | 0.32 | 0.74 | 19 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1299 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1162 Ų buried · 10 hydrogen bonds · protein-protein
- C–E · 950 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 881 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 760 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6EHP · The crystal structure of the human LAMTOR complex · 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 A 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 0.98
- 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 0.80
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 6EHP · PDBe 6EHP · UniProt Q9UHA4 · UniProt Q9Y2Q5 · UniProt O43504 · UniProt Q0VGL1 · UniProt Q6IAA8
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