MolNFT v1 · #77864 · protein
S. cerevisiae DBP5 L327V bound to GLE1 H337R and IP6
3RRN · ATP-dependent RNA helicase DBP5: “S. cerevisiae DBP5 L327V bound to GLE1 H337R and IP6”. X-ray diffraction, 2 ligands (IHP, ADP), 9 pockets (best druggability 0.80). MolNFT v1 #77864 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3RRN
- Type
- protein
- Length
- 682 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, ADP
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent RNA helicase DBP5 (EC 3.6.4.13) | protein | 389 | 38% helix, 17% strand | P20449 |
| B | Nucleoporin GLE1 | protein | 293 | 76% helix, 1% strand | Q12315 |
Ligands and binding sites
- IHP · Inositol hexakisphosphate · ligand · 3 copies · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1135 | 0.80 | 0.81 | 98 | ADP |
| 2 | 981 | 0.76 | 0.79 | 66 | IHP |
| 3 | 102 | 0.58 | 0.86 | 27 | empty |
| 4 | 67 | 0.38 | 0.79 | 13 | empty |
| 5 | 67 | 0.36 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1647 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3RRN · S. cerevisiae dbp5 l327v bound to gle1 h337r 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 0.84
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 3RRN · PDBe 3RRN · UniProt P20449 · UniProt Q12315
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