Research workbench
Structure of the conserved yeast listerin (LTN1) selenomethionine- substituted N-terminal domain, trigonal form
Analyse Structure of the conserved yeast listerin (LTN1) selenomethionine- substituted… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FG1
- Type
- protein
- Length
- 406 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase listerin
- EC
- 6.3.2.-
- UniProt
- Q04781
- Ligands
- K
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase listerin (EC 6.3.2.-) | protein | 406 | 71% helix, 0% strand | Q04781 |
Ligands and binding sites
- K · Potassium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 294 | 0.67 | 0.82 | 25 | empty |
| 2 | 67 | 0.42 | 0.81 | 14 | empty |
| 3 | 87 | 0.40 | 0.78 | 19 | empty |
| 4 | 82 | 0.37 | 0.77 | 16 | empty |
| 5 | 84 | 0.34 | 0.74 | 25 | empty |
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 5FG1 · Structure of the conserved yeast listerin (Ltn1) selenomethionine-substituted N-terminal… · 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 5FG1 · PDBe 5FG1 · UniProt Q04781
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