MolNFT v1 · #34274 · protein + RNA
Structural basis for RNA unwinding by the dead-box protein drosophila vasa
2DB3 · 5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3': “Structural basis for RNA unwinding by the dead-box protein drosophila vasa”. X-ray diffraction, 2 ligands (ANP, MG), 19 pockets (best druggability 0.84). MolNFT v1 #34274 on GenesisL1: 3D…
- PDB
- 2DB3
- Type
- protein + RNA
- Length
- 1,705 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3'; ATP-dependent RNA helicase vasa
- EC
- 3.6.1.3
- UniProt
- P09052
- Ligands
- ANP, MG
- Pockets
- 19 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | 5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3' | rna | 5 | — | — |
| F, G | 5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3' | rna | 7 | — | — |
| H | 5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3' | rna | 6 | — | — |
| A, B, C, D | ATP-dependent RNA helicase vasa (EC 3.6.1.3) | protein | 420 | 40% helix, 15% strand | P09052 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1134 | 0.84 | 0.85 | 125 | MG, ANP |
| 2 | 766 | 0.81 | 0.84 | 84 | MG, ANP |
| 3 | 885 | 0.80 | 0.82 | 84 | MG, ANP |
| 4 | 234 | 0.75 | 0.89 | 44 | MG, ANP |
| 5 | 574 | 0.71 | 0.80 | 49 | empty |
Interfaces
6 interfaces between chains.
- A–B · 635 Ų buried · 6 hydrogen bonds · protein-protein
- H–D · 633 Ų buried · 27 hydrogen bonds · protein-nucleic
- F–B · 632 Ų buried · 24 hydrogen bonds · protein-nucleic
- G–C · 631 Ų buried · 25 hydrogen bonds · protein-nucleic
- E–A · 591 Ų buried · 23 hydrogen bonds · protein-nucleic
Compared structures
- 2DB3 · Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa · the same entry in another collection · chain D against D, TM-score 1.00
- P09052 · AlphaFold monomer V2.0 prediction for ATP-dependent RNA helicase vasa (P09052) · 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 P09052
- Elsewhere: RCSB PDB 2DB3 · PDBe 2DB3 · UniProt P09052
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