Research workbench
Crystal structure of the bombyx mori vasa helicase (E339Q) in complex with RNA and amppnp
Analyse Crystal structure of the bombyx mori vasa helicase (E339Q) in complex with RNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 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
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