MolNFT v1 · #106124 · protein
The 1.35A structure of a viral RNase L antagonist reveals basis for the 2'-5'-oligoadenylate binding and enzyme activity.
4RPT · Capping enzyme protein: “The 1.35A structure of a viral RNase L antagonist reveals basis for the 2'-5'-oligoadenylate binding and…”. X-ray diffraction, 6 pockets (best druggability 0.72). MolNFT v1 #106124 on GenesisL1: 3D…
- PDB
- 4RPT
- Type
- protein
- Length
- 284 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capping enzyme protein
- UniProt
- B3F2X4
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capping enzyme protein | protein | 144 | 22% helix, 38% strand | B3F2X4 |
| B | Capping enzyme protein | protein | 140 | 22% helix, 39% strand | B3F2X4 |
Ligands and binding sites
- MLI · Malonate ion · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.72 | 0.97 | 19 | MLI |
| 2 | 300 | 0.55 | 0.75 | 29 | EDO |
| 3 | 288 | 0.54 | 0.75 | 31 | EDO |
| 4 | 224 | 0.51 | 0.76 | 40 | empty |
| 5 | 50 | 0.28 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1152 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4RPT · The 1.35A structure of a viral RNase L antagonist reveals basis for the… · 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 B3F2X4
- Elsewhere: RCSB PDB 4RPT · PDBe 4RPT · UniProt B3F2X4
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