MolNFT v1 · #92456 · protein
Active state of intact sensor domain of human RNase L with 2-5A bound
4G8L · 2-5A-dependent ribonuclease: “Active state of intact sensor domain of human RNase L with 2-5A bound”. X-ray diffraction, 1 ligand (25A), 10 pockets (best druggability 0.57). MolNFT v1 #92456 on GenesisL1: 3D structure, binding sites…
- PDB
- 4G8L
- Type
- protein
- Length
- 1,195 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-5A-dependent ribonuclease
- EC
- 3.1.26.-
- UniProt
- Q05823
- Ligands
- 25A
- Pockets
- 10 · best druggability 0.57
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-5A-dependent ribonuclease (EC 3.1.26.-) | protein | 307 | 51% helix, 2% strand | Q05823 |
| B | 2-5A-dependent ribonuclease (EC 3.1.26.-) | protein | 294 | 51% helix, 2% strand | Q05823 |
| C | 2-5A-dependent ribonuclease (EC 3.1.26.-) | protein | 300 | 52% helix, 2% strand | Q05823 |
| D | 2-5A-dependent ribonuclease (EC 3.1.26.-) | protein | 294 | 51% helix, 2% strand | Q05823 |
Ligands and binding sites
- 25A · 5'-O-monophosphoryladenylyl(2'->5')adenylyl(2'->5') adenosine · ligand · 4 copies · chains A, B, C, D
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 | 454 | 0.57 | 0.74 | 47 | empty |
| 2 | 197 | 0.52 | 0.77 | 32 | 25A |
| 3 | 239 | 0.51 | 0.75 | 30 | 25A |
| 4 | 152 | 0.46 | 0.76 | 17 | empty |
| 5 | 133 | 0.44 | 0.76 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–B · 884 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 856 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 297 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 36 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4G8L · Active state of intact sensor domain of human RNase L with 2-5A bound · the same entry in another collection · chain D against D, TM-score 1.00
- Q05823 · AlphaFold monomer V2.0 prediction for 2-5A-dependent ribonuclease (Q05823) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q05823
- Elsewhere: RCSB PDB 4G8L · PDBe 4G8L · UniProt Q05823
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