Research workbench
Structure of TREX1 in complex with a nucleotide and inhibitor ions (sodium and zinc)
Analyse Structure of TREX1 in complex with a nucleotide and inhibitor ions (sodium and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3B6P
- 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, ZN, NA
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 42% 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 | 42% helix, 17% strand | Q91XB0 |
Ligands and binding sites
- TMP · Thymidine-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- NA · Sodium 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 | 853 | 0.74 | 0.79 | 88 | empty |
| 2 | 454 | 0.65 | 0.78 | 47 | empty |
| 3 | 197 | 0.55 | 0.79 | 30 | TMP, NA |
| 4 | 215 | 0.53 | 0.77 | 31 | TMP, NA |
| 5 | 211 | 0.53 | 0.77 | 27 | TMP, NA |
Interfaces
5 interfaces between chains.
- B–D · 1794 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 1774 Ų buried · 36 hydrogen bonds · protein-protein
- A–D · 273 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 147 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 36 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3B6P · Structure of TREX1 in complex with a nucleotide and inhibitor ions (sodium and zinc) · 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 3B6P · PDBe 3B6P · UniProt Q91XB0
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