MolNFT v1 · #153980 · protein
Yeast NPL4 in complex with LYS48-linked diubiquitin
6JWI · Ubiqutin: “Yeast NPL4 in complex with LYS48-linked diubiquitin”. X-ray diffraction, 3 ligands (BCN, GLC, ZN), 18 pockets (best druggability 0.77). MolNFT v1 #153980 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6JWI
- Type
- protein
- Length
- 1,061 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiqutin; Nuclear protein localization protein 4
- UniProt
- A5JUZ1, P33755
- Ligands
- BCN, GLC, ZN
- Pockets
- 18 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I | Ubiqutin | protein | 72 | 17% helix, 32% strand | A5JUZ1 |
| A | Nuclear protein localization protein 4 | protein | 459 | 32% helix, 22% strand | P33755 |
| E | Nuclear protein localization protein 4 | protein | 459 | 32% helix, 21% strand | P33755 |
| G | Ubiqutin | protein | 71 | 17% helix, 34% strand | A5JUZ1 |
Ligands and binding sites
- BCN · Bicine · ligand · 9 copies · chains A, E
- GLC · alpha-D-glucopyranose · sugar · 28 copies · chains A, E
- ZN · Zinc ion · metal · 4 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1113 | 0.77 | 0.79 | 94 | GLC |
| 2 | 321 | 0.69 | 0.83 | 53 | empty |
| 3 | 403 | 0.62 | 0.77 | 38 | empty |
| 4 | 136 | 0.61 | 0.85 | 28 | empty |
| 5 | 189 | 0.48 | 0.76 | 34 | empty |
Interfaces
5 interfaces between chains.
- A–E · 726 Ų buried · 4 hydrogen bonds · protein-protein
- I–A · 498 Ų buried · 8 hydrogen bonds · protein-protein
- A–G · 484 Ų buried · 7 hydrogen bonds · protein-protein
- I–G · 375 Ų buried · 3 hydrogen bonds · protein-protein
- I–E · 265 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (engineered).
Compared structures
- 6JWI · Yeast Npl4 in complex with Lys48-linked diubiquitin · the same entry in another collection · chain I against I, TM-score 1.00
- P33755 · AlphaFold monomer V2.0 prediction for nuclear protein localization protein 4 (P33755) · 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 A5JUZ1
- Every structure of UniProt P33755
- Elsewhere: RCSB PDB 6JWI · PDBe 6JWI · UniProt A5JUZ1 · UniProt P33755
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.