Research workbench
Crystal structure of RNase L in complex with myricetin
Analyse Crystal structure of RNase L in complex with myricetin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ELW
- Type
- protein
- Length
- 1,351 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease L
- UniProt
- A5H025
- Ligands
- 25L, MYC, PO4
- Pockets
- 19 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| a | Ribonuclease L | protein | 675 | 51% helix, 8% strand | A5H025 |
| b | Ribonuclease L | protein | 676 | 50% helix, 8% strand | A5H025 |
Ligands and binding sites
- 25L · [[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-[[(2R,3R,4R, 5R)-5-(6-aminopurin-9-yl)-4-[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-3-hydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-3-hydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] phosphono hydrogen phosphate · ligand · 2 copies · chains a, b
- MYC · 3,5,7-trihydroxy-2-(3,4,5-trihydroxyphenyl)-4H-chromen-4-one · ligand · 2 copies · chains a, b
- PO4 · Phosphate ion · ion · chains a, b
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 751 | 0.76 | 0.81 | 90 | empty |
| 2 | 998 | 0.73 | 0.76 | 63 | 25L |
| 3 | 1149 | 0.72 | 0.76 | 79 | 25L |
| 4 | 778 | 0.70 | 0.77 | 70 | empty |
| 5 | 189 | 0.65 | 0.85 | 32 | MYC |
Interfaces
1 interface between chains.
- a–b · 3709 Ų buried · 55 hydrogen bonds · protein-protein
Compared structures
- 7ELW · Crystal structure of RNase L in complex with Myricetin · the same entry in another collection · chain a 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 A5H025
- Elsewhere: RCSB PDB 7ELW · PDBe 7ELW · UniProt A5H025
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