Research workbench
The structural basis of the interaction between nonsense mediated decay factors UPF2 and UPF3
Analyse The structural basis of the interaction between nonsense mediated decay factors… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UW4
- Type
- protein
- Length
- 678 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UPF3X; Regulator of nonsense transcripts 2
- UniProt
- Q9BZI7, Q9HAU5
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | UPF3X | protein | 91 | 20% helix, 35% strand | Q9BZI7 |
| B, D | Regulator of nonsense transcripts 2 | protein | 248 | 71% helix, 0% strand | Q9HAU5 |
Ligands and binding sites
- BME · Beta-mercaptoethanol · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 961 | 0.83 | 0.84 | 97 | empty |
| 2 | 138 | 0.41 | 0.75 | 29 | BME |
| 3 | 78 | 0.35 | 0.76 | 20 | empty |
| 4 | 101 | 0.33 | 0.73 | 21 | empty |
| 5 | 54 | 0.29 | 0.74 | 9 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1117 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1111 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 819 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 237 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 236 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct).
Compared structures
- 1UW4 · The structural basis of the interaction between nonsense mediated decay factors UPF2 and… · 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 1.00
- Q9BZI7 · AlphaFold monomer V2.0 prediction for regulator of nonsense transcripts 3B (Q9BZI7) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q9BZI7
- Every structure of UniProt Q9HAU5
- Elsewhere: RCSB PDB 1UW4 · PDBe 1UW4 · UniProt Q9BZI7 · UniProt Q9HAU5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.