Research workbench
Crystal structure of human heteroheptameric complex
Analyse Crystal structure of human heteroheptameric complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5X6V
- Type
- protein
- Length
- 780 residues
- Chains
- 7
- 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, Q7L523, Q99K70
- Ligands
- NA
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 7 distinct chains · 41% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ragulator complex protein LAMTOR3 | protein | 121 | 40% helix, 31% strand | Q9UHA4 |
| B | Ragulator complex protein LAMTOR2 | protein | 125 | 43% helix, 30% strand | Q9Y2Q5 |
| C | Ragulator complex protein LAMTOR5 | protein | 91 | 29% helix, 37% strand | O43504 |
| D | Ragulator complex protein LAMTOR4 | protein | 85 | 21% helix, 42% strand | Q0VGL1 |
| E | Ragulator complex protein LAMTOR1 | protein | 108 | 55% helix, 1% strand | Q6IAA8 |
| F | RAS-related GTP-binding protein a | protein | 118 | 42% helix, 28% strand | Q7L523 |
| G | RAS-related GTP-binding protein C | protein | 132 | 46% helix, 23% strand | Q99K70 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 723 | 0.75 | 0.80 | 65 | empty |
| 2 | 624 | 0.70 | 0.78 | 59 | empty |
| 3 | 113 | 0.42 | 0.77 | 22 | empty |
| 4 | 131 | 0.42 | 0.75 | 21 | empty |
| 5 | 116 | 0.40 | 0.75 | 16 | empty |
Interfaces
15 interfaces between chains.
- A–B · 1429 Ų buried · 23 hydrogen bonds · protein-protein
- F–G · 1347 Ų buried · 23 hydrogen bonds · protein-protein
- A–E · 1158 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1001 Ų buried · 19 hydrogen bonds · protein-protein
- C–E · 996 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5X6V · Crystal structure of human heteroheptameric complex · the same entry in another collection · chain G against G, TM-score 1.00
- Q99K70 · AlphaFold monomer V2.0 prediction for RAS-related GTP-binding protein C (Q99K70) · a predicted model of the same protein · chain G 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
- 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 0.96
- 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 0.95
- 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 0.95
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
- Every structure of UniProt Q7L523
- Every structure of UniProt Q99K70
- Elsewhere: RCSB PDB 5X6V · PDBe 5X6V · UniProt Q9UHA4 · UniProt Q9Y2Q5 · UniProt O43504 · UniProt Q0VGL1 · UniProt Q6IAA8 · UniProt Q7L523 · UniProt Q99K70
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