MolNFT v1 · #23772 · protein
Crystal structure of the rala-gppnhp-SEC5 ral-binding domain complex
1UAD · RAS-related protein ral-a: “Crystal structure of the rala-gppnhp-SEC5 ral-binding domain complex”. X-ray diffraction, 2 ligands (GNP, MG), 10 pockets (best druggability 0.75). MolNFT v1 #23772 on GenesisL1: 3D structure, binding…
- PDB
- 1UAD
- Type
- protein
- Length
- 530 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein ral-a; Exocyst complex component SEC5
- UniProt
- P11233, O54921
- Ligands
- GNP, MG
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RAS-related protein ral-a | protein | 173 | 40% helix, 25% strand | P11233 |
| C, D | Exocyst complex component SEC5 | protein | 92 | 7% helix, 47% strand | O54921 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 527 | 0.75 | 0.83 | 58 | empty |
| 2 | 356 | 0.63 | 0.79 | 41 | MG, GNP |
| 3 | 316 | 0.62 | 0.79 | 41 | MG, GNP |
| 4 | 139 | 0.45 | 0.76 | 24 | empty |
| 5 | 148 | 0.40 | 0.74 | 18 | empty |
Interfaces
5 interfaces between chains.
- A–C · 567 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 498 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 413 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 347 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 314 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1UAD · Crystal structure of the RalA-GppNHp-Sec5 Ral-binding domain complex · the same entry in another collection · chain A against A, TM-score 1.00
- P11233 · AlphaFold monomer V2.0 prediction for RAS-related protein ral-a (P11233) · a predicted model of the same protein · chain A against A, TM-score 0.99
- O54921 · AlphaFold monomer V2.0 prediction for exocyst complex component 2 (O54921) · 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 P11233
- Every structure of UniProt O54921
- Elsewhere: RCSB PDB 1UAD · PDBe 1UAD · UniProt P11233 · UniProt O54921
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