MolNFT v1 · #58533 · protein
Structure of TREX1 in complex with a nucleotide and an inhibitor ion (lithium)
3B6O · Three prime repair exonuclease 1: “Structure of TREX1 in complex with a nucleotide and an inhibitor ion (lithium)”. X-ray diffraction, 2 ligands (TMP, LI), 7 pockets (best druggability 0.74). MolNFT v1 #58533 on GenesisL1: 3D…
- PDB
- 3B6O
- Type
- protein
- Length
- 868 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Three prime repair exonuclease 1
- EC
- 3.1.11.2
- UniProt
- Q91XB0
- Ligands
- TMP, LI
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Three prime repair exonuclease 1 (EC 3.1.11.2) | protein | 217 | 40% helix, 17% strand | Q91XB0 |
Ligands and binding sites
- TMP · Thymidine-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- LI · Lithium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 829 | 0.74 | 0.79 | 93 | empty |
| 2 | 461 | 0.66 | 0.78 | 49 | empty |
| 3 | 212 | 0.55 | 0.79 | 29 | TMP, LI |
| 4 | 233 | 0.55 | 0.78 | 31 | TMP, LI |
| 5 | 214 | 0.54 | 0.78 | 29 | TMP, LI |
Interfaces
5 interfaces between chains.
- B–D · 1794 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 1791 Ų buried · 40 hydrogen bonds · protein-protein
- A–D · 283 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 133 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 34 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3B6O · Structure of TREX1 in complex with a nucleotide and an inhibitor ion (lithium) · the same entry in another collection · chain A against A, TM-score 1.00
- Q91XB0 · AlphaFold monomer V2.0 prediction for three-prime repair exonuclease 1 (Q91XB0) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q91XB0
- Elsewhere: RCSB PDB 3B6O · PDBe 3B6O · UniProt Q91XB0
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