MolNFT v1 · #156347 · protein
Crystal structure of RNase L in complex with SU11652
6M12 · Ribonuclease L: “Crystal structure of RNase L in complex with SU11652”. X-ray diffraction, 3 ligands (J60, 25L, PO4), 18 pockets (best druggability 0.78). MolNFT v1 #156347 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6M12
- Type
- protein
- Length
- 1,365 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease L
- UniProt
- A5H025
- Ligands
- J60, 25L, PO4
- Pockets
- 18 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| a | Ribonuclease L | protein | 681 | 51% helix, 8% strand | A5H025 |
| b | Ribonuclease L | protein | 684 | 50% helix, 7% strand | A5H025 |
Ligands and binding sites
- J60 · 5-[(E)-(5-chloro-2-oxo-1,2-dihydro-3H-indol-3-ylidene) methyl]-N-[2-(diethylamino)ethyl]-2,4-dimethyl-1H-pyrrole-3-carboxamide · ligand · 2 copies · chains a, b
- 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
- 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 984 | 0.78 | 0.80 | 111 | empty |
| 2 | 864 | 0.74 | 0.78 | 81 | 25L |
| 3 | 816 | 0.73 | 0.78 | 58 | 25L |
| 4 | 680 | 0.68 | 0.77 | 64 | empty |
| 5 | 237 | 0.64 | 0.83 | 34 | J60 |
Interfaces
1 interface between chains.
- a–b · 3772 Ų buried · 71 hydrogen bonds · protein-protein
Compared structures
- 6M12 · Crystal Structure of Rnase L in complex with SU11652 · 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 6M12 · PDBe 6M12 · UniProt A5H025
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