Research workbench
Cryo-EM structure of the NLRP3 decamer bound to the inhibitor CRID3
Analyse Cryo-EM structure of the NLRP3 decamer bound to the inhibitor CRID3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PZC
- Type
- protein
- Length
- 9,060 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nacht, lrr and pyd domains-containing protein 3
- UniProt
- Q96P20
- Ligands
- ADP, 8GI
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 2 distinct chains · 44% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H | Nacht, lrr and pyd domains-containing protein 3 | protein | 1010 | 45% helix, 7% strand | Q96P20 |
| B, C, D, E, F, G, I, J | Nacht, lrr and pyd domains-containing protein 3 | protein | 880 | 43% helix, 8% strand | Q96P20 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- 8GI · 1-(1,2,3,5,6,7-hexahydro-s-indacen-4-yl)-3-[4-(2-oxidanylpropan-2-yl)furan-2-yl]sulfonyl-urea · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1177 | 0.88 | 0.89 | 139 | ADP |
| 2 | 880 | 0.86 | 0.88 | 84 | ADP |
| 3 | 889 | 0.86 | 0.87 | 82 | ADP |
| 4 | 915 | 0.85 | 0.87 | 86 | ADP |
| 5 | 873 | 0.85 | 0.87 | 77 | ADP |
Interfaces
13 interfaces between chains.
- G–H · 1182 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 1173 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 1163 Ų buried · 6 hydrogen bonds · protein-protein
- I–J · 1157 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1156 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7PZC · Cryo-EM structure of the NLRP3 decamer bound to the inhibitor CRID3 · the same entry in another collection · chain J against J, TM-score 1.00
- Q96P20 · AlphaFold monomer V2.0 prediction for nacht, lrr and pyd domains- containing protein 3… · a predicted model of the same protein · chain B against A, TM-score 0.65
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 Q96P20
- Elsewhere: RCSB PDB 7PZC · PDBe 7PZC · UniProt Q96P20
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