Research workbench
Structure of the conserved yeast listerin (Ltn1) N-terminal domain, MONOCLINIC FORM
Analyse Structure of the conserved yeast listerin (Ltn1) N-terminal domain, MONOCLINIC… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FG0
- Type
- protein
- Length
- 814 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.41
- Source
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
- Molecule
- E3 ubiquitin-protein ligase listerin
- EC
- 6.3.2.-
- UniProt
- Q04781
- Ligands
- K
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · resolution 2.41 · 1 distinct chain · 69% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | E3 ubiquitin-protein ligase listerin (EC 6.3.2.-) | protein | 407 | 69% helix, 0% strand | Q04781 |
Ligands and binding sites
- K · Potassium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 522 | 0.74 | 0.82 | 42 | empty |
| 2 | 820 | 0.73 | 0.78 | 70 | empty |
| 3 | 259 | 0.66 | 0.83 | 24 | empty |
| 4 | 283 | 0.65 | 0.81 | 24 | empty |
| 5 | 152 | 0.48 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 725 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5FG0 · Structure of the conserved yeast listerin (LTN1) N-terminal domain, monoclinic form · the same entry in another collection · chain A against A, TM-score 1.00
- Q04781 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase listerin (Q04781) · 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 Q04781
- Elsewhere: RCSB PDB 5FG0 · PDBe 5FG0 · UniProt Q04781
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