MolNFT v1 · #88670 · protein + RNA
Crystal structure of the bombyx mori vasa helicase (E339Q) in complex with RNA,ADP and pi
4D26 · Bmvlg protein: “Crystal structure of the bombyx mori vasa helicase (E339Q) in complex with RNA,ADP and pi”. X-ray diffraction, 3 ligands (ADP, MG, PO4), 5 pockets (best druggability 0.77). MolNFT v1 #88670 on GenesisL1: 3D…
- PDB
- 4D26
- Type
- protein + RNA
- Length
- 436 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bmvlg protein; 5'-R(*UP*GP*AP*CP*AP*UP)-3'
- UniProt
- O01378
- Ligands
- ADP, MG, PO4
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bmvlg protein | protein | 430 | 39% helix, 17% strand | O01378 |
| D | 5'-R(*UP*GP*AP*CP*AP*UP)-3' | rna | 6 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 702 | 0.77 | 0.82 | 78 | ADP, PO4, MG |
| 2 | 247 | 0.65 | 0.83 | 25 | empty |
| 3 | 92 | 0.44 | 0.79 | 23 | empty |
| 4 | 90 | 0.35 | 0.75 | 17 | empty |
| 5 | 73 | 0.30 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–D · 675 Ų buried · 24 hydrogen bonds · protein-nucleic
Compared structures
- 4D26 · Crystal structure of the Bombyx mori Vasa helicase (E339Q) in complex with RNA,ADP and Pi · the same entry in another collection · chain A against A, TM-score 1.00
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 O01378
- Elsewhere: RCSB PDB 4D26 · PDBe 4D26 · UniProt O01378
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