MolNFT v1 · #178836 · protein
Human DPP9-CARD8 complex
7JN7 · Dipeptidyl peptidase 9: “Human DPP9-CARD8 complex”. Electron microscopy, 1 ligand (GK2), 20 pockets (best druggability 0.83). MolNFT v1 #178836 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7JN7
- Type
- protein
- Length
- 2,044 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase 9; Caspase recruitment domain-containing protein 8
- EC
- 3.4.14.5
- UniProt
- Q86TI2, Q9Y2G2
- Ligands
- GK2
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 15% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dipeptidyl peptidase 9 (EC 3.4.14.5) | protein | 846 | 18% helix, 33% strand | Q86TI2 |
| B | Caspase recruitment domain-containing protein 8 | protein | 272 | 6% helix, 37% strand | Q9Y2G2 |
| C | Caspase recruitment domain-containing protein 8 | protein | 127 | 8% helix, 30% strand | Q9Y2G2 |
| D | Dipeptidyl peptidase 9 (EC 3.4.14.5) | protein | 799 | 17% helix, 32% strand | Q86TI2 |
Ligands and binding sites
- GK2 · [(2~{R})-1-[(2~{R})-2-azanyl-3-methyl-butanoyl]pyrrolidin-2-yl]boronic acid · ligand · 2 copies · chains A, D
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 | 176 | 0.83 | 0.97 | 33 | empty |
| 2 | 443 | 0.81 | 0.89 | 58 | empty |
| 3 | 448 | 0.78 | 0.86 | 66 | GK2 |
| 4 | 320 | 0.78 | 0.89 | 53 | empty |
| 5 | 186 | 0.77 | 0.93 | 39 | empty |
Interfaces
4 interfaces between chains.
- A–D · 2134 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 959 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 807 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 438 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7JN7 · Human DPP9-CARD8 complex · the same entry in another collection · chain D against D, 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
- Q9Y2G2 · AlphaFold monomer V2.0 prediction for caspase recruitment domain- containing protein 8… · a predicted model of the same protein · chain B against A, TM-score 0.91
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 Q9Y2G2
- Elsewhere: RCSB PDB 7JN7 · PDBe 7JN7 · UniProt Q86TI2 · UniProt Q9Y2G2
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