Research workbench
The crystal structure of RANBPM/9 ius-spry domain in complex with ddx- 4 peptide
Analyse The crystal structure of RANBPM/9 ius-spry domain in complex with ddx- 4 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JIU
- Type
- protein
- Length
- 430 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ran-binding protein 9; Probable ATP-dependent RNA helicase DDX4
- EC
- 3.6.4.13
- UniProt
- Q96S59, Q61496
- Ligands
- CL
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ran-binding protein 9 | protein | 209 | 13% helix, 37% strand | Q96S59 |
| C, D | Probable ATP-dependent RNA helicase DDX4 (EC 3.6.4.13) | protein | 6 | 0% helix, 0% strand | Q61496 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 132 | 0.60 | 0.85 | 29 | CL |
| 2 | 187 | 0.48 | 0.76 | 16 | empty |
| 3 | 61 | 0.30 | 0.75 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 524 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 343 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 300 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5JIU · The crystal structure of RanBPM/9 IUS-SPRY domain in complex with DDX-4 peptide · the same entry in another collection · chain A against A, TM-score 1.00
- Q96S59 · AlphaFold monomer V2.0 prediction for ran-binding protein 9 (Q96S59) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q61496 · AlphaFold monomer V2.0 prediction for ATP-dependent RNA helicase DDX4 (Q61496) · a predicted model of the same protein · chain D against A, TM-score 0.68
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 Q96S59
- Every structure of UniProt Q61496
- Elsewhere: RCSB PDB 5JIU · PDBe 5JIU · UniProt Q96S59 · UniProt Q61496
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