Research workbench
S. cerevisiae DBP5 L327V bound to RNA and ADP BEF3
Analyse S. cerevisiae DBP5 L327V bound to RNA and ADP BEF3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PEW
- Type
- protein + RNA
- Length
- 396 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent RNA helicase DBP5; RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
- EC
- 3.6.4.13
- UniProt
- P20449
- Ligands
- ADP, BEF, MG, NO3
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent RNA helicase DBP5 (EC 3.6.4.13) | protein | 391 | 41% helix, 17% strand | P20449 |
| B | RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3') | rna | 5 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- BEF · Beryllium trifluoride ion · ligand · chains A
- MG · Magnesium ion · metal · 3 copies · chains A
- NO3 · Nitrate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 242 | 0.64 | 0.83 | 36 | ADP, MG, BEF |
| 2 | 221 | 0.61 | 0.82 | 35 | empty |
| 3 | 73 | 0.36 | 0.77 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 679 Ų buried · 22 hydrogen bonds · protein-nucleic
Compared structures
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 P20449
- Elsewhere: RCSB PDB 3PEW · PDBe 3PEW · UniProt P20449
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