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Crystal structure of nova-2 KH3 K-homology RNA-binding domain bound to 20-mer RNA hairpin
Analyse Crystal structure of nova-2 KH3 K-homology RNA-binding domain bound to 20-mer… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EC6
- Type
- protein + RNA
- Length
- 211 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 20-mer RNA hairpin; RNA-binding protein nova-2
- UniProt
- Q9UNW9
- Pockets
- 3 · best druggability 0.50
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | 20-mer RNA hairpin | rna | 20 | — | — |
| A | RNA-binding protein nova-2 | protein | 87 | 52% helix, 22% strand | Q9UNW9 |
| B | RNA-binding protein nova-2 | protein | 84 | 52% helix, 23% strand | Q9UNW9 |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.50 | 0.76 | 28 | empty |
| 2 | 93 | 0.30 | 0.73 | 13 | empty |
| 3 | 50 | 0.27 | 0.74 | 11 | empty |
Interfaces
3 interfaces between chains.
- C–B · 996 Ų buried · 25 hydrogen bonds · protein-nucleic
- D–A · 953 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–B · 478 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1EC6 · Crystal structure of nova-2 KH3 K-homology RNA-binding domain bound to 20-mer RNA hairpin · the same entry in another collection · chain C against C, TM-score 1.00
- Q9UNW9 · AlphaFold monomer V2.0 prediction for RNA-binding protein nova-2 (Q9UNW9) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 Q9UNW9
- Elsewhere: RCSB PDB 1EC6 · PDBe 1EC6 · UniProt Q9UNW9
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