MolNFT v1 · #101782 · protein
Crystal structure of RNase L in complex with 2-5A and AMP-pnp
4O1P · Ribonuclease L: “Crystal structure of RNase L in complex with 2-5A and AMP-pnp”. X-ray diffraction, 3 ligands (ANP, 25L, MG), 20 pockets (best druggability 0.77). MolNFT v1 #101782 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4O1P
- Type
- protein
- Length
- 2,684 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease L
- UniProt
- A5H025
- Ligands
- ANP, 25L, MG
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease L | protein | 672 | 51% helix, 7% strand | A5H025 |
| B | Ribonuclease L | protein | 671 | 51% helix, 7% strand | A5H025 |
| C | Ribonuclease L | protein | 673 | 51% helix, 7% strand | A5H025 |
| D | Ribonuclease L | protein | 668 | 50% helix, 7% strand | A5H025 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains A, B, C, D
- 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
- MG · Magnesium ion · metal · 8 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 | 576 | 0.77 | 0.84 | 88 | empty |
| 2 | 786 | 0.76 | 0.81 | 80 | empty |
| 3 | 542 | 0.76 | 0.84 | 79 | empty |
| 4 | 761 | 0.75 | 0.80 | 75 | empty |
| 5 | 1081 | 0.74 | 0.77 | 68 | 25L |
Interfaces
5 interfaces between chains.
- A–B · 3996 Ų buried · 59 hydrogen bonds · protein-protein
- C–D · 3914 Ų buried · 58 hydrogen bonds · protein-protein
- B–C · 505 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 190 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 71 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4O1P · Crystal Structure of RNase L in complex with 2-5A and AMP-PNP · 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 4O1P · PDBe 4O1P · UniProt A5H025
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