Research workbench
S. cerevisiae DBP5 L327V bound to NUP159, GLE1 H337R, IP6 and ADP
Analyse S. cerevisiae DBP5 L327V bound to NUP159, GLE1 H337R, IP6 and ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RRM
- Type
- protein
- Length
- 1,040 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent RNA helicase DBP5; Nucleoporin GLE1; Nucleoporin NUP159
- EC
- 3.6.4.13
- UniProt
- P20449, Q12315, P40477
- Ligands
- ADP, IHP, MG
- Pockets
- 13 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent RNA helicase DBP5 (EC 3.6.4.13) | protein | 375 | 42% helix, 19% strand | P20449 |
| B | Nucleoporin GLE1 | protein | 295 | 75% helix, 1% strand | Q12315 |
| C | Nucleoporin NUP159 | protein | 370 | 4% helix, 49% strand | P40477 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- IHP · Inositol hexakisphosphate · ligand · chains A, B
- MG · Magnesium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1137 | 0.84 | 0.85 | 140 | ADP, MG |
| 2 | 69 | 0.73 | 0.98 | 18 | empty |
| 3 | 409 | 0.63 | 0.78 | 44 | empty |
| 4 | 174 | 0.59 | 0.82 | 31 | empty |
| 5 | 151 | 0.56 | 0.82 | 25 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1463 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 1084 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 3RRM · S. cerevisiae dbp5 l327v bound to nup159, gle1 h337r, ip6 and adp · the same entry in another collection · chain A against A, TM-score 1.00
- P40477 · AlphaFold monomer V2.0 prediction for nucleoporin NUP159 (P40477) · a predicted model of the same protein · chain C against A, TM-score 0.99
- 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 0.73
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
- Every structure of UniProt P40477
- Elsewhere: RCSB PDB 3RRM · PDBe 3RRM · UniProt P20449 · UniProt Q12315 · UniProt P40477
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