Research workbench
Structural evidence for feedback activation by rasgtp of the RAS-specific nucleotide exchange factor sos
Analyse Structural evidence for feedback activation by rasgtp of the RAS-specific… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NVW
- Type
- protein
- Length
- 801 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transforming protein P21/H-RAS-1; Son of sevenless protein homolog 1
- UniProt
- P01112, Q07889
- Ligands
- GNP, MG, PO4
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Q, R | Transforming protein P21/H-RAS-1 | protein | 166 | 35% helix, 27% strand | P01112 |
| S | Son of sevenless protein homolog 1 | protein | 469 | 59% helix, 4% strand | Q07889 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains Q
- MG · Magnesium ion · metal · chains Q
- PO4 · Phosphate ion · ion · 7 copies · chains Q, S, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1135 | 0.83 | 0.84 | 130 | MG, PO4, GNP |
| 2 | 296 | 0.63 | 0.80 | 39 | empty |
| 3 | 206 | 0.51 | 0.76 | 31 | empty |
| 4 | 189 | 0.48 | 0.76 | 35 | PO4 |
| 5 | 102 | 0.39 | 0.76 | 20 | empty |
Interfaces
2 interfaces between chains.
- R–S · 1904 Ų buried · 29 hydrogen bonds · protein-protein
- Q–S · 1604 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 1NVW · Structural evidence for feedback activation by RasGTP of the Ras-specific nucleotide… · the same entry in another collection · chain Q against Q, TM-score 1.00
- Q07889 · AlphaFold monomer V2.0 prediction for son of sevenless homolog 1 (Q07889) · a predicted model of the same protein · chain S against A, TM-score 0.92
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 P01112
- Every structure of UniProt Q07889
- Elsewhere: RCSB PDB 1NVW · PDBe 1NVW · UniProt P01112 · UniProt Q07889
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