Research workbench
Crystal structure of RNase L in complex with KM05073
Analyse Crystal structure of RNase L in complex with KM05073 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DSY
- Type
- protein
- Length
- 1,348 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease L
- UniProt
- A5H025
- Ligands
- 25A, HFX, PO4
- Pockets
- 18 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| a | Ribonuclease L | protein | 672 | 50% helix, 8% strand | A5H025 |
| b | Ribonuclease L | protein | 676 | 49% helix, 7% strand | A5H025 |
Ligands and binding sites
- 25A · 5'-O-monophosphoryladenylyl(2'->5')adenylyl(2'->5') adenosine · ligand · 2 copies · chains a, b
- HFX · 1-chloranyl-3-methylsulfinyl-6,7-dihydro-5H-2-benzothiophen-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
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1109 | 0.77 | 0.79 | 114 | empty |
| 2 | 1008 | 0.72 | 0.76 | 63 | 25A |
| 3 | 1176 | 0.72 | 0.76 | 80 | 25A |
| 4 | 816 | 0.71 | 0.77 | 76 | empty |
| 5 | 242 | 0.65 | 0.83 | 34 | HFX |
Interfaces
1 interface between chains.
- a–b · 3718 Ų buried · 57 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7DSY · Crystal Structure of RNase L in complex with KM05073 · 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 7DSY · PDBe 7DSY · UniProt A5H025
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