Research workbench
Crystal structure of the first MIF4G domain of human nonsense mediated decay factor UPF2
Analyse Crystal structure of the first MIF4G domain of human nonsense mediated decay… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CEM
- Type
- protein
- Length
- 617 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.6
- Source
- HOMO SAPIENS
- Molecule
- Regulator of nonsense transcripts 2
- UniProt
- Q9HAU5
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · resolution 2.6 · 2 distinct chains · 73% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Regulator of nonsense transcripts 2 | protein | 308 | 72% helix, 1% strand | Q9HAU5 |
| B | Regulator of nonsense transcripts 2 | protein | 309 | 73% helix, 1% strand | Q9HAU5 |
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 777 | 0.76 | 0.80 | 81 | empty |
| 2 | 172 | 0.62 | 0.84 | 25 | empty |
| 3 | 207 | 0.62 | 0.82 | 26 | empty |
| 4 | 136 | 0.52 | 0.80 | 15 | empty |
| 5 | 123 | 0.48 | 0.79 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 378 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 4CEM · Crystal structure of the first MIF4G domain of human nonsense mediated decay factor UPF2 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HAU5 · AlphaFold monomer V2.0 prediction for regulator of nonsense transcripts 2 (Q9HAU5) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q9HAU5
- Elsewhere: RCSB PDB 4CEM · PDBe 4CEM · UniProt Q9HAU5
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