Research workbench
Crystal structure of the UPF2-interacting domain of nonsense mediated mRNA decay factor UPF1
Analyse Crystal structure of the UPF2-interacting domain of nonsense mediated mRNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IYK
- Type
- protein
- Length
- 310 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Regulator of nonsense transcripts 1
- EC
- 3.6.1.-
- UniProt
- Q92900
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Regulator of nonsense transcripts 1 (EC 3.6.1.-) | protein | 155 | 21% helix, 17% strand | Q92900 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.64 | 0.94 | 15 | empty |
| 2 | 364 | 0.56 | 0.74 | 29 | empty |
| 3 | 226 | 0.50 | 0.76 | 27 | empty |
| 4 | 179 | 0.44 | 0.74 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 465 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2IYK · Crystal structure of the UPF2-interacting domain of nonsense mediated mRNA decay factor… · the same entry in another collection · chain A against A, 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 0.97
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
- Elsewhere: RCSB PDB 2IYK · PDBe 2IYK · UniProt Q92900
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