Research workbench
Crystal structures of NLRP14 pyrin domain reveal a conformational switch mechanism, regulating its molecular interactions
Analyse Crystal structures of NLRP14 pyrin domain reveal a conformational switch… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4N1J
- Type
- protein
- Length
- 368 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nacht, lrr and pyd domains-containing protein 14
- UniProt
- Q86W24
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 81% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nacht, lrr and pyd domains-containing protein 14 | protein | 91 | 81% helix, 0% strand | Q86W24 |
| B | Nacht, lrr and pyd domains-containing protein 14 | protein | 94 | 80% helix, 0% strand | Q86W24 |
| C | Nacht, lrr and pyd domains-containing protein 14 | protein | 89 | 84% helix, 0% strand | Q86W24 |
| D | Nacht, lrr and pyd domains-containing protein 14 | protein | 94 | 80% helix, 0% strand | Q86W24 |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 457 | 0.69 | 0.80 | 49 | empty |
| 2 | 163 | 0.45 | 0.75 | 22 | empty |
| 3 | 82 | 0.38 | 0.77 | 21 | empty |
| 4 | 68 | 0.34 | 0.76 | 18 | empty |
| 5 | 55 | 0.30 | 0.75 | 13 | empty |
Interfaces
6 interfaces between chains.
- A–B · 983 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 981 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 565 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 390 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 265 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 4N1J · Crystal structures of NLRP14 pyrin domain reveal a conformational switch mechanism… · the same entry in another collection · chain D against D, TM-score 1.00
- Q86W24 · AlphaFold monomer V2.0 prediction for nacht, lrr and pyd domains- containing protein 14… · a predicted model of the same protein · chain D against A, TM-score 0.77
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 Q86W24
- Elsewhere: RCSB PDB 4N1J · PDBe 4N1J · UniProt Q86W24
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