MolNFT v1 · #113753 · protein + RNA
Structure of mle RNA ADP ALF4 complex
5AOR · Dosage compensation regulator: “Structure of mle RNA ADP ALF4 complex”. X-ray diffraction, 3 ligands (ADP, ALF, MG), 20 pockets (best druggability 0.90). MolNFT v1 #113753 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5AOR
- Type
- protein + RNA
- Length
- 2,021 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dosage compensation regulator; 5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP)-3'
- EC
- 3.6.4.13
- UniProt
- P24785
- Ligands
- ADP, ALF, MG
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dosage compensation regulator (EC 3.6.4.13) | protein | 1009 | 45% helix, 17% strand | P24785 |
| B | Dosage compensation regulator (EC 3.6.4.13) | protein | 992 | 46% helix, 17% strand | P24785 |
| C, D | 5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP)-3' | rna | 10 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- ALF · Tetrafluoroaluminate ion · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 914 | 0.90 | 0.93 | 146 | empty |
| 2 | 1197 | 0.89 | 0.91 | 157 | GOL |
| 3 | 271 | 0.79 | 0.91 | 50 | empty |
| 4 | 514 | 0.79 | 0.86 | 66 | ADP, MG, ALF |
| 5 | 156 | 0.76 | 0.93 | 40 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1724 Ų buried · 38 hydrogen bonds · protein-nucleic
- B–D · 1714 Ų buried · 38 hydrogen bonds · protein-nucleic
- A–B · 717 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- P24785 · AlphaFold monomer V2.0 prediction for dosage compensation regulator (P24785) · a predicted model of the same protein · chain B 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 P24785
- Elsewhere: RCSB PDB 5AOR · PDBe 5AOR · UniProt P24785
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