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Crystal structure of RNase L in complex with 2-5A
Analyse Crystal structure of RNase L in complex with 2-5A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4O1O
- Type
- protein
- Length
- 2,687 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease L
- UniProt
- A5H025
- Ligands
- 25L
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Ribonuclease L | protein | 672 | 50% helix, 8% strand | A5H025 |
| C | Ribonuclease L | protein | 671 | 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 · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 678 | 0.76 | 0.81 | 67 | empty |
| 2 | 1124 | 0.73 | 0.76 | 67 | 25L |
| 3 | 1117 | 0.73 | 0.76 | 73 | 25L |
| 4 | 1158 | 0.73 | 0.76 | 70 | 25L |
| 5 | 614 | 0.73 | 0.80 | 67 | empty |
Interfaces
5 interfaces between chains.
- C–D · 4040 Ų buried · 68 hydrogen bonds · protein-protein
- A–B · 3951 Ų buried · 68 hydrogen bonds · protein-protein
- A–D · 531 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 190 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 52 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4O1O · Crystal Structure of RNase L in complex with 2-5A · 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 4O1O · PDBe 4O1O · UniProt A5H025
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