MolNFT v1 · #118900 · protein
Structure of the conserved yeast listerin (LTN1) N-terminal domain, monoclinic form
5FG0 · E3 ubiquitin-protein ligase listerin: “Structure of the conserved yeast listerin (LTN1) N-terminal domain, monoclinic form”. X-ray diffraction, 1 ligand (K), 9 pockets (best druggability 0.74). MolNFT v1 #118900 on GenesisL1: 3D…
- PDB
- 5FG0
- Type
- protein
- Length
- 814 residues
- Chains
- 2
- 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
- 9 · best druggability 0.74
Structure
x-ray diffraction · 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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