MolNFT v1 · #153981 · protein
NPL4 in complex with UFD1
6JWJ · Nuclear protein localization protein 4: “NPL4 in complex with UFD1”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.67). MolNFT v1 #153981 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6JWJ
- Type
- protein
- Length
- 485 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear protein localization protein 4; Peptide from ubiquitin fusion degradation protein…
- UniProt
- P33755, P53044
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear protein localization protein 4 | protein | 466 | 31% helix, 22% strand | P33755 |
| C | Peptide from ubiquitin fusion degradation protein 1 | protein | 19 | 0% helix, 21% strand | P53044 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 113 | 0.67 | 0.90 | 34 | GOL |
| 2 | 318 | 0.54 | 0.75 | 45 | GOL |
| 3 | 145 | 0.46 | 0.76 | 23 | empty |
| 4 | 50 | 0.33 | 0.78 | 16 | empty |
| 5 | 75 | 0.32 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–C · 1127 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6JWJ · Npl4 in complex with Ufd1 · the same entry in another collection · chain A against A, 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 0.99
- P53044 · AlphaFold monomer V2.0 prediction for ubiquitin fusion degradation protein 1 (P53044) · a predicted model of the same protein · chain C against A, TM-score 0.36
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 P33755
- Every structure of UniProt P53044
- Elsewhere: RCSB PDB 6JWJ · PDBe 6JWJ · UniProt P33755 · UniProt P53044
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