MolNFT v2 · #226586 · protein
Co-crystal structure of human TREX1 in complex with an inhibitor
9AVA · Three-prime repair exonuclease 1: “Co-crystal structure of human TREX1 in complex with an inhibitor”. X-ray diffraction at 2.3, 3 ligands (A1AG1, K, UNX), 20 pockets (best druggability 0.84). MolNFT v2 #226586 on GenesisL1: 3D…
- PDB
- 9AVA
- Type
- protein
- Length
- 2,525 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- Homo sapiens
- Molecule
- Three-prime repair exonuclease 1
- EC
- 3.1.11.2
- UniProt
- Q9NSU2
- Ligands
- A1AG1, K, UNX
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · resolution 2.3 · 9 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Three-prime repair exonuclease 1 (EC 3.1.11.2) | protein | 211 | 40% helix, 17% strand | Q9NSU2 |
| B | Three-prime repair exonuclease 1 (EC 3.1.11.2) | protein | 210 | 40% helix, 17% strand | Q9NSU2 |
| C | Three-prime repair exonuclease 1 (EC 3.1.11.2) | protein | 207 | 42% helix, 17% strand | Q9NSU2 |
| D, G | Three-prime repair exonuclease 1 (EC 3.1.11.2) | protein | 212 | 41% helix, 17% strand | Q9NSU2 |
| E | Three-prime repair exonuclease 1 (EC 3.1.11.2) | protein | 210 | 40% helix, 17% strand | Q9NSU2 |
| H | Three-prime repair exonuclease 1 (EC 3.1.11.2) | protein | 210 | 40% helix, 17% strand | Q9NSU2 |
| I, J | Three-prime repair exonuclease 1 (EC 3.1.11.2) | protein | 211 | 41% helix, 17% strand | Q9NSU2 |
| K | Three-prime repair exonuclease 1 (EC 3.1.11.2) | protein | 211 | 41% helix, 18% strand | Q9NSU2 |
| L | Three-prime repair exonuclease 1 (EC 3.1.11.2) | protein | 209 | 40% helix, 17% strand | Q9NSU2 |
Ligands and binding sites
- A1AG1 · (2R)-2-[(5R,6S,8R,9aS)-8-amino-1-oxo-5-(2-phenylethyl)hexahydro-1H-pyrrolo[1,2-a][1,4]diazepin-2(3H)-yl]-N-[(3,4-dichlorophenyl)methyl]-4-methylpentanamide · ligand · 12 copies · chains A, B, K, C, H, D, E, F, I, G, J, L
- K · Potassium ion · metal · 11 copies · chains A, B, C, D, F, G, H, I, J, K, L
- UNX · Unknown atom or ion · ion · 29 copies · chains A, B, K, C, H, D, E, F, I, G, J, L
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 | 965 | 0.84 | 0.85 | 95 | K, A1AG1, UNX |
| 2 | 1151 | 0.81 | 0.83 | 81 | K, A1AG1 |
| 3 | 1100 | 0.81 | 0.82 | 73 | K, A1AG1 |
| 4 | 366 | 0.72 | 0.84 | 68 | empty |
| 5 | 407 | 0.68 | 0.81 | 77 | empty |
Interfaces
19 interfaces between chains.
- C–E · 1680 Ų buried · 46 hydrogen bonds · protein-protein
- G–H · 1676 Ų buried · 43 hydrogen bonds · protein-protein
- A–D · 1671 Ų buried · 42 hydrogen bonds · protein-protein
- K–L · 1668 Ų buried · 43 hydrogen bonds · protein-protein
- B–F · 1668 Ų buried · 42 hydrogen bonds · protein-protein
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 Q9NSU2
- Elsewhere: RCSB PDB 9AVA · PDBe 9AVA · UniProt Q9NSU2
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