MolNFT v1 · #53075 · protein
Crystal structure of the complex between human nonsense mediated decay factors UPF1 and UPF2
2WJV · Regulator of nonsense transcripts 1: “Crystal structure of the complex between human nonsense mediated decay factors UPF1 and UPF2”. X-ray diffraction, 2 ligands (ZN, SO4), 18 pockets (best druggability 0.78). MolNFT v1 #53075 on…
- 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
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