MolNFT v1 · #144420 · protein
Crystal structure of rheb in complex with compound 1 at 1.65A resolution
6BSX · GTP-binding protein rheb: “Crystal structure of rheb in complex with compound 1 at 1.65A resolution”. X-ray diffraction, 3 ligands (GDP, E7S, MG), 12 pockets (best druggability 0.75). MolNFT v1 #144420 on GenesisL1: 3D structure…
- PDB
- 6BSX
- Type
- protein
- Length
- 676 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTP-binding protein rheb
- UniProt
- Q15382
- Ligands
- GDP, E7S, MG
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | GTP-binding protein rheb | protein | 170 | 37% helix, 26% strand | Q15382 |
| C | GTP-binding protein rheb | protein | 168 | 38% helix, 27% strand | Q15382 |
| D | GTP-binding protein rheb | protein | 168 | 37% helix, 26% strand | Q15382 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- E7S · (5,6-dimethyl-1H-benzimidazol-2-yl)methanol · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1119 | 0.75 | 0.78 | 97 | MG, GDP, E7S |
| 2 | 135 | 0.49 | 0.79 | 26 | MG, GDP |
| 3 | 111 | 0.47 | 0.79 | 20 | EDO |
| 4 | 117 | 0.43 | 0.77 | 25 | MG, GDP |
| 5 | 110 | 0.43 | 0.78 | 25 | MG, GDP |
Interfaces
4 interfaces between chains.
- A–B · 498 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 446 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 201 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 13 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6BSX · Crystal structure of rheb in complex with compound 1 at 1.65A resolution · the same entry in another collection · chain B against B, TM-score 1.00
- Q15382 · AlphaFold monomer V2.0 prediction for GTP-binding protein rheb (Q15382) · a predicted model of the same protein · chain C against A, TM-score 0.96
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 Q15382
- Elsewhere: RCSB PDB 6BSX · PDBe 6BSX · UniProt Q15382
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