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
- 1NVV
- 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
- 11 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Q | Transforming protein P21/H-RAS-1 | protein | 166 | 38% helix, 27% strand | P01112 |
| R | Transforming protein P21/H-RAS-1 | protein | 166 | 37% helix, 25% strand | P01112 |
| S | Son of sevenless protein homolog 1 | protein | 469 | 60% 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 · 5 copies · chains Q, R, S
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1169 | 0.84 | 0.85 | 140 | MG, GNP, PO4 |
| 2 | 299 | 0.62 | 0.80 | 34 | PO4 |
| 3 | 256 | 0.53 | 0.76 | 47 | PO4 |
| 4 | 239 | 0.53 | 0.76 | 31 | empty |
| 5 | 82 | 0.38 | 0.77 | 17 | empty |
Interfaces
2 interfaces between chains.
- R–S · 1864 Ų buried · 25 hydrogen bonds · protein-protein
- Q–S · 1671 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 1NVV · 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 1NVV · PDBe 1NVV · UniProt P01112 · UniProt Q07889
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