Research workbench
The crystal structure of the human lamtor-raga ctd-ragc ctd complex
Analyse The crystal structure of the human lamtor-raga ctd-ragc ctd complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EHR
- Type
- protein
- Length
- 794 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, Q9HB90
- Pockets
- 12 · best druggability 0.72
Structure
x-ray diffraction · 7 distinct chains · 39% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ragulator complex protein LAMTOR3 | protein | 120 | 41% helix, 29% strand | Q9UHA4 |
| B | Ragulator complex protein LAMTOR2 | protein | 126 | 34% helix, 29% strand | Q9Y2Q5 |
| C | Ragulator complex protein LAMTOR5 | protein | 91 | 31% helix, 37% strand | O43504 |
| D | Ragulator complex protein LAMTOR4 | protein | 97 | 25% helix, 35% strand | Q0VGL1 |
| E | Ragulator complex protein LAMTOR1 | protein | 115 | 52% helix, 2% strand | Q6IAA8 |
| F | RAS-related GTP-binding protein a | protein | 110 | 41% helix, 29% strand | Q7L523 |
| G | RAS-related GTP-binding protein C | protein | 135 | 42% helix, 24% strand | Q9HB90 |
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 724 | 0.72 | 0.78 | 69 | empty |
| 2 | 530 | 0.71 | 0.80 | 44 | empty |
| 3 | 306 | 0.64 | 0.80 | 31 | empty |
| 4 | 386 | 0.61 | 0.77 | 58 | empty |
| 5 | 127 | 0.47 | 0.78 | 25 | empty |
Interfaces
15 interfaces between chains.
- A–B · 1329 Ų buried · 20 hydrogen bonds · protein-protein
- F–G · 1239 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 1105 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 1086 Ų buried · 22 hydrogen bonds · protein-protein
- C–E · 995 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6EHR · The crystal structure of the human LAMTOR-RagA CTD-RagC CTD complex · the same entry in another collection · chain G against G, 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
- Q7L523 · AlphaFold monomer V2.0 prediction for RAS-related GTP-binding protein a (Q7L523) · a predicted model of the same protein · chain F against A, TM-score 0.96
- Q9HB90 · AlphaFold monomer V2.0 prediction for RAS-related GTP-binding protein C (Q9HB90) · a predicted model of the same protein · chain G 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 0.94
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 Q9HB90
- Elsewhere: RCSB PDB 6EHR · PDBe 6EHR · UniProt Q9UHA4 · UniProt Q9Y2Q5 · UniProt O43504 · UniProt Q0VGL1 · UniProt Q6IAA8 · UniProt Q7L523 · UniProt Q9HB90
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