MolNFT v1 · #75054 · protein
S. cerevisiae DBP5 L327V C-terminal domain bound to GLE1 and IP6
3PEV · ATP-dependent RNA helicase DBP5: “S. cerevisiae DBP5 L327V C-terminal domain bound to GLE1 and IP6”. X-ray diffraction, 2 ligands (IHP, SO4), 6 pockets (best druggability 0.75). MolNFT v1 #75054 on GenesisL1: 3D structure, binding…
- PDB
- 3PEV
- Type
- protein
- Length
- 473 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent RNA helicase DBP5; Nucleoporin GLE1
- EC
- 3.6.4.13
- UniProt
- P20449, Q12315
- Ligands
- IHP, SO4
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 61% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent RNA helicase DBP5 (EC 3.6.4.13) | protein | 178 | 39% helix, 21% strand | P20449 |
| B | Nucleoporin GLE1 | protein | 295 | 74% helix, 1% strand | Q12315 |
Ligands and binding sites
- IHP · Inositol hexakisphosphate · ligand · chains A, B
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 898 | 0.75 | 0.79 | 71 | IHP |
| 2 | 97 | 0.60 | 0.88 | 26 | empty |
| 3 | 69 | 0.38 | 0.78 | 15 | GOL |
| 4 | 60 | 0.37 | 0.79 | 15 | empty |
| 5 | 91 | 0.36 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1095 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 modified (engineered).
Compared structures
- 3PEV · S. cerevisiae Dbp5 L327V C-terminal domain bound to Gle1 and IP6 · the same entry in another collection · chain A against A, TM-score 1.00
- Q12315 · AlphaFold monomer V2.0 prediction for nucleoporin GLE1 (Q12315) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P20449 · AlphaFold monomer V2.0 prediction for ATP-dependent RNA helicase DBP5 (P20449) · a predicted model of the same protein · chain A against A, TM-score 0.88
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
- Every structure of UniProt Q12315
- Elsewhere: RCSB PDB 3PEV · PDBe 3PEV · UniProt P20449 · UniProt Q12315
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