Research workbench
Structure of human Usb1 with uridine 5'-monophosphate
Analyse Structure of human Usb1 with uridine 5'-monophosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V1M
- Type
- protein
- Length
- 185 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.47
- Source
- Homo sapiens
- Molecule
- U6 snRNA phosphodiesterase
- EC
- 3.1.4.-
- UniProt
- Q9BQ65
- Ligands
- U5P, CL
- Pockets
- 2 · best druggability 0.51
Structure
x-ray diffraction · resolution 1.47 · 1 distinct chain · 34% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | U6 snRNA phosphodiesterase (EC 3.1.4.-) | protein | 185 | 34% helix, 32% strand | Q9BQ65 |
Ligands and binding sites
- U5P · Uridine-5'-monophosphate · ligand · chains A
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 250 | 0.51 | 0.75 | 33 | GOL, U5P |
| 2 | 67 | 0.40 | 0.79 | 16 | GOL |
Compared structures
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 5V1M · PDBe 5V1M · UniProt Q9BQ65
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