MolNFT v1 · #149112 · protein + RNA
Crystal structure of danio rerio LIN41 filamin-nhl domains in complex with mab-10 3'UTR 13MER RNA
6FQL · E3 ubiquitin-protein ligase TRIM71: “Crystal structure of danio rerio LIN41 filamin-nhl domains in complex with mab-10 3'UTR 13MER RNA”. X-ray diffraction, 1 ligand (CL), 4 pockets (best druggability 0.72). MolNFT v1 #149112 on…
- PDB
- 6FQL
- Type
- protein + RNA
- Length
- 403 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase TRIM71; RNA (5'-R(*UP*GP*CP*AP*UP*UP*UP*AP*AP*UP*GP*CP*A)-3')
- EC
- 2.3.2.27
- UniProt
- E7FAM5
- Ligands
- CL
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase TRIM71 (EC 2.3.2.27) | protein | 390 | 7% helix, 47% strand | E7FAM5 |
| B | RNA (5'-R(*UP*GP*CP*AP*UP*UP*UP*AP*AP*UP*GP*CP*A)-3') | rna | 13 | — | — |
Ligands and binding sites
- CL · Chloride ion · ion · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 423 | 0.72 | 0.82 | 38 | empty |
| 2 | 95 | 0.43 | 0.79 | 16 | CL |
| 3 | 97 | 0.39 | 0.77 | 19 | CL |
| 4 | 90 | 0.38 | 0.76 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 502 Ų buried · 25 hydrogen bonds · protein-nucleic
Compared structures
- 6FQL · Crystal structure of Danio rerio Lin41 filamin-NHL domains in complex with mab-10 3'UTR… · the same entry in another collection · chain A against A, TM-score 1.00
- E7FAM5 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase TRIM71 (E7FAM5) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 E7FAM5
- Elsewhere: RCSB PDB 6FQL · PDBe 6FQL · UniProt E7FAM5
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