MolNFT v1 · #88669 · protein + RNA
Crystal structure of the bombyx mori vasa helicase (E339Q) in complex with RNA and amppnp
4D25 · Bmvlg protein: “Crystal structure of the bombyx mori vasa helicase (E339Q) in complex with RNA and amppnp”. X-ray diffraction, 2 ligands (ANP, MG), 5 pockets (best druggability 0.74). MolNFT v1 #88669 on GenesisL1: 3D structure…
- PDB
- 4D25
- Type
- protein + RNA
- Length
- 433 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
- ANP, MG
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bmvlg protein | protein | 427 | 41% helix, 17% strand | O01378 |
| D | 5'-R(*UP*GP*AP*CP*AP*UP)-3' | rna | 6 | — | — |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- MG · Magnesium ion · metal · chains A
- GOL · Glycerol · additive · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 201 | 0.74 | 0.90 | 38 | ANP, MG |
| 2 | 472 | 0.66 | 0.78 | 49 | empty |
| 3 | 247 | 0.64 | 0.82 | 25 | GOL |
| 4 | 85 | 0.44 | 0.80 | 20 | empty |
| 5 | 94 | 0.39 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–D · 673 Ų buried · 25 hydrogen bonds · protein-nucleic
Compared structures
- 4D25 · Crystal structure of the Bombyx mori Vasa helicase (E339Q) in complex with RNA and AMPPNP · 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 4D25 · PDBe 4D25 · UniProt O01378
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.