MolNFT v1 · #169262 · protein
Cryo-EM structure of NLRP1-DPP9 complex
6X6A · Dipeptidyl peptidase 9: “Cryo-EM structure of NLRP1-DPP9 complex”. Electron microscopy, 20 pockets (best druggability 0.85). MolNFT v1 #169262 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6X6A
- Type
- protein
- Length
- 2,524 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase 9; Nacht, lrr and pyd domains-containing protein 1
- EC
- 3.4.14.5
- UniProt
- Q86TI2, Q9C000
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 15% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Dipeptidyl peptidase 9 (EC 3.4.14.5) | protein | 846 | 19% helix, 33% strand | Q86TI2 |
| B, E | Nacht, lrr and pyd domains-containing protein 1 | protein | 134 | 3% helix, 31% strand | Q9C000 |
| G, I | Nacht, lrr and pyd domains-containing protein 1 | protein | 138 | 9% helix, 33% strand | Q9C000 |
| C, F | Nacht, lrr and pyd domains-containing protein 1 | protein | 144 | 11% helix, 27% strand | Q9C000 |
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1091 | 0.85 | 0.86 | 100 | empty |
| 2 | 508 | 0.83 | 0.90 | 71 | empty |
| 3 | 169 | 0.83 | 0.98 | 32 | empty |
| 4 | 306 | 0.79 | 0.90 | 54 | empty |
| 5 | 623 | 0.78 | 0.84 | 67 | empty |
Interfaces
15 interfaces between chains.
- A–D · 2124 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1848 Ų buried · 14 hydrogen bonds · protein-protein
- B–G · 1834 Ų buried · 19 hydrogen bonds · protein-protein
- E–I · 1817 Ų buried · 16 hydrogen bonds · protein-protein
- D–F · 1797 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6X6A · Cryo-EM structure of NLRP1-DPP9 complex · the same entry in another collection · chain F against F, TM-score 1.00
- Q86TI2 · AlphaFold monomer V2.0 prediction for dipeptidyl peptidase 9 (Q86TI2) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q9C000 · AlphaFold monomer V2.0 prediction for nacht, lrr and pyd domains- containing protein 1… · a predicted model of the same protein · chain G against A, TM-score 0.89
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 Q86TI2
- Every structure of UniProt Q9C000
- Elsewhere: RCSB PDB 6X6A · PDBe 6X6A · UniProt Q86TI2 · UniProt Q9C000
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.