Research workbench
Structural and functional insights into the human UPF1 helicase core
Analyse Structural and functional insights into the human UPF1 helicase core in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GK6
- Type
- protein
- Length
- 1,204 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
- ADP, MG, PO4
- Pockets
- 14 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Regulator of nonsense transcripts 1 (EC 3.6.1.-) | protein | 602 | 38% helix, 18% strand | Q92900 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1142 | 0.74 | 0.77 | 84 | MG, PO4, ADP |
| 2 | 1197 | 0.74 | 0.77 | 87 | MG, PO4, ADP |
| 3 | 839 | 0.74 | 0.78 | 72 | empty |
| 4 | 272 | 0.58 | 0.78 | 36 | empty |
| 5 | 162 | 0.47 | 0.76 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 789 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2GK6 · Structural and Functional insights into the human Upf1 helicase core · 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 2GK6 · PDBe 2GK6 · UniProt Q92900
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