Research workbench
Crystal structure (II) of nova-1 KH1/KH2 domain tandem with 25NT RNA hairpin
Analyse Crystal structure (II) of nova-1 KH1/KH2 domain tandem with 25NT RNA hairpin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ANR
- Type
- protein + RNA
- Length
- 180 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*CP*(5BU) P*CP*GP*CP*GP*GP*AP*UP*CP*AP*GP*UP*CP*AP*CP*CP*CP*AP*AP*GP*CP*GP*AP*G…
- UniProt
- P51513
- Ligands
- MG, K
- Pockets
- 2 · best druggability 0.34
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-R(*CP*(5BU) P*CP*GP*CP*GP*GP*AP*UP*CP*AP*GP*UP*CP*AP*CP*CP*CP*AP*AP*GP*CP*GP*AP*G )-3' | rna | 25 | — | — |
| A | Neuro-oncological ventral antigen 1 | protein | 155 | 49% helix, 25% strand | P51513 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.34 | 0.76 | 13 | empty |
| 2 | 72 | 0.28 | 0.74 | 11 | K, MG |
Interfaces
1 interface between chains.
- B–A · 620 Ų buried · 16 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 3 modified (engineered, nucleotide modification).
Compared structures
- 2ANR · Crystal structure (II) of Nova-1 KH1/KH2 domain tandem with 25nt RNA hairpin · the same entry in another collection · chain B against B, TM-score 1.00
- P51513 · AlphaFold monomer V2.0 prediction for RNA-binding protein nova-1 (P51513) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P51513
- Elsewhere: RCSB PDB 2ANR · PDBe 2ANR · UniProt P51513
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.