Research workbench
Structure of human USB1 with uridine-adenosine, inactive H208Q mutant
Analyse Structure of human USB1 with uridine-adenosine, inactive H208Q mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D2Z
- Type
- protein + RNA
- Length
- 190 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- U6 snrna phosphodiesterase; 5'-R(UP*A)-3')
- EC
- 3.1.4.-
- UniProt
- Q9BQ65
- Ligands
- CL
- Pockets
- 1 · best druggability 0.37
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | U6 snrna phosphodiesterase (EC 3.1.4.-) | protein | 188 | 35% helix, 31% strand | Q9BQ65 |
| C | 5'-R(UP*A)-3') | rna | 2 | — | — |
Ligands and binding sites
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.37 | 0.77 | 19 | empty |
Interfaces
1 interface between chains.
- A–C · 464 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 6D2Z · Structure of human Usb1 with uridine-adenosine, inactive H208Q mutant · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BQ65 · AlphaFold monomer V2.0 prediction for U6 snrna phosphodiesterase (Q9BQ65) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9BQ65
- Elsewhere: RCSB PDB 6D2Z · PDBe 6D2Z · UniProt Q9BQ65
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