Research workbench
Crystal structure of the complex between human nonsense mediated decay factors UPF1 and UPF2
Analyse Crystal structure of the complex between human 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
- 2WJV
- Type
- protein
- Length
- 1,654 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Regulator of nonsense transcripts 1; Regulator of nonsense transcripts 2
- EC
- 3.6.1.-
- UniProt
- Q92900, Q9HAU5
- Ligands
- ZN, SO4
- Pockets
- 18 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Regulator of nonsense transcripts 1 (EC 3.6.1.-) | protein | 772 | 36% helix, 18% strand | Q92900 |
| B | Regulator of nonsense transcripts 1 (EC 3.6.1.-) | protein | 768 | 37% helix, 18% strand | Q92900 |
| D | Regulator of nonsense transcripts 2 | protein | 54 | 44% helix, 26% strand | Q9HAU5 |
| E | Regulator of nonsense transcripts 2 | protein | 60 | 35% helix, 33% strand | Q9HAU5 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 851 | 0.78 | 0.81 | 76 | SO4 |
| 2 | 782 | 0.76 | 0.80 | 71 | SO4 |
| 3 | 166 | 0.62 | 0.84 | 25 | SO4 |
| 4 | 170 | 0.54 | 0.79 | 29 | empty |
| 5 | 89 | 0.53 | 0.85 | 20 | empty |
Interfaces
3 interfaces between chains.
- B–E · 1834 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 1760 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 893 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 2WJV · Crystal structure of the complex between human nonsense mediated decay factors UPF1 and… · the same entry in another collection · chain E against E, TM-score 1.00
- Q92900 · AlphaFold monomer V2.0 prediction for regulator of nonsense transcripts 1 (Q92900) · a predicted model of the same protein · chain A against A, TM-score 0.76
- Q9HAU5 · AlphaFold monomer V2.0 prediction for regulator of nonsense transcripts 2 (Q9HAU5) · a predicted model of the same protein · chain E against A, TM-score 0.50
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 Q92900
- Every structure of UniProt Q9HAU5
- Elsewhere: RCSB PDB 2WJV · PDBe 2WJV · UniProt Q92900 · UniProt Q9HAU5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.