Research workbench
The crystal structure and mutational analysis of a novel RNA-binding domain found in the human tap nuclear mRNA export factor
Analyse The crystal structure and mutational analysis of a novel RNA-binding domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KOO
- Type
- protein
- Length
- 854 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tip associating protein
- UniProt
- Q9UBU9
- Pockets
- 10 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tip associating protein | protein | 258 | 24% helix, 13% strand | Q9UBU9 |
| B | Tip associating protein | protein | 165 | 22% helix, 8% strand | Q9UBU9 |
| C | Tip associating protein | protein | 262 | 18% helix, 13% strand | Q9UBU9 |
| D | Tip associating protein | protein | 169 | 28% helix, 10% strand | Q9UBU9 |
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 842 | 0.85 | 0.87 | 103 | empty |
| 2 | 765 | 0.82 | 0.85 | 71 | empty |
| 3 | 101 | 0.73 | 0.95 | 23 | empty |
| 4 | 120 | 0.65 | 0.89 | 26 | empty |
| 5 | 176 | 0.59 | 0.82 | 34 | empty |
Interfaces
5 interfaces between chains.
- A–D · 883 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 873 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 689 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 686 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 527 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 1KOO · The crystal structure and mutational analysis of a novel RNA-binding domain found in the… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9UBU9 · AlphaFold monomer V2.0 prediction for nuclear RNA export factor 1 (Q9UBU9) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q9UBU9
- Elsewhere: RCSB PDB 1KOO · PDBe 1KOO · UniProt Q9UBU9
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