Research workbench
Choanoflagellate salpingoeca rosetta RAS with GDP bound
Analyse Choanoflagellate salpingoeca rosetta RAS with GDP bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WDS
- Type
- protein
- Length
- 337 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS protein
- EC
- 3.6.5.2
- UniProt
- F2UBE5
- Ligands
- GDP, MG
- Pockets
- 4 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS protein (EC 3.6.5.2) | protein | 169 | 38% helix, 25% strand | F2UBE5 |
| B | RAS protein (EC 3.6.5.2) | protein | 168 | 39% helix, 26% strand | F2UBE5 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
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 | 247 | 0.52 | 0.76 | 31 | GOL |
| 2 | 179 | 0.51 | 0.78 | 25 | empty |
| 3 | 141 | 0.48 | 0.78 | 31 | GDP, MG |
| 4 | 137 | 0.46 | 0.77 | 30 | GDP, MG |
Interfaces
1 interface between chains.
- A–B · 722 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5WDS · Choanoflagellate Salpingoeca rosetta Ras with GDP bound · the same entry in another collection · chain A against A, TM-score 1.00
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 F2UBE5
- Elsewhere: RCSB PDB 5WDS · PDBe 5WDS · UniProt F2UBE5
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