Research workbench
Crystal structures of ral-gppnhp and ral-GDP reveal two novel binding sites that are also present in RAS and rap
Analyse Crystal structures of ral-gppnhp and ral-GDP reveal two novel binding sites… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1U8Y
- Type
- protein
- Length
- 322 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein ral-a
- UniProt
- P63320
- Ligands
- GNP, MG
- Pockets
- 4 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related protein ral-a | protein | 154 | 37% helix, 26% strand | P63320 |
| B | RAS-related protein ral-a | protein | 168 | 38% helix, 24% strand | P63320 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 229 | 0.54 | 0.77 | 38 | MG, GNP |
| 2 | 185 | 0.49 | 0.77 | 28 | MG, GNP |
| 3 | 70 | 0.32 | 0.75 | 15 | empty |
| 4 | 68 | 0.29 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 540 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1U8Y · CRystal structures of Ral-GppNHp and Ral-GDP reveal two novel binding sites that are also… · the same entry in another collection · chain A against A, TM-score 1.00
- P63320 · AlphaFold monomer V2.0 prediction for RAS-related protein ral-a (P63320) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P63320
- Elsewhere: RCSB PDB 1U8Y · PDBe 1U8Y · UniProt P63320
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