MolNFT v1 · #57621 · protein + RNA
Structure of arabidopsis HYL1 and its molecular implications for miRNA processing
3ADI · F21M12.9 protein: “Structure of arabidopsis HYL1 and its molecular implications for miRNA processing”. X-ray diffraction, 4 pockets (best druggability 0.48). MolNFT v1 #57621 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3ADI
- Type
- protein + RNA
- Length
- 233 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- F21M12.9 protein; RNA (5'-R(P*CP*UP*CP*GP*AP*UP*AP*AP*CP*C)-3'); RNA…
- UniProt
- O04492
- Pockets
- 4 · best druggability 0.48
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | F21M12.9 protein | protein | 71 | 38% helix, 28% strand | O04492 |
| D | RNA (5'-R(P*CP*UP*CP*GP*AP*UP*AP*AP*CP*C)-3') | rna | 10 | — | — |
| E | RNA (5'-R(*GP*GP*UP*UP*AP*UP*CP*GP*AP*G)-3') | rna | 10 | — | — |
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 260 | 0.48 | 0.73 | 24 | empty |
| 2 | 111 | 0.48 | 0.80 | 23 | empty |
| 3 | 50 | 0.30 | 0.76 | 11 | empty |
| 4 | 57 | 0.29 | 0.75 | 12 | empty |
Interfaces
6 interfaces between chains.
- D–E · 473 Ų buried · 40 hydrogen bonds · nucleic-nucleic
- A–C · 408 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 385 Ų buried · 1 hydrogen bond · protein-protein
- A–E · 241 Ų buried · 3 hydrogen bonds · protein-nucleic
- A–D · 152 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 3ADI · Structure of Arabidopsis HYL1 and its molecular implications for miRNA processing · the same entry in another collection · chain E against E, TM-score 1.00
- O04492 · AlphaFold monomer V2.0 prediction for double-stranded RNA-binding protein 1 (O04492) · a predicted model of the same protein · chain C against A, TM-score 0.93
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 O04492
- Elsewhere: RCSB PDB 3ADI · PDBe 3ADI · UniProt O04492
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