Research workbench
The crystal structure of TREX1 explains the 3' nucleotide specificity and reveals a polyproline II helix for protein partenring
Analyse The crystal structure of TREX1 explains the 3' nucleotide specificity and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IOC
- Type
- protein
- Length
- 438 residues
- Chains
- 2
- 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
- D5M, MN
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Three prime repair exonuclease 1 (EC 3.1.11.2) | protein | 220 | 40% helix, 16% strand | Q91XB0 |
| A | Three prime repair exonuclease 1 (EC 3.1.11.2) | protein | 218 | 40% helix, 17% strand | Q91XB0 |
Ligands and binding sites
- D5M · 2'-deoxyadenosine-5'-monophosphate · ligand · 2 copies · chains B, A
- MN · Manganese (II) ion · metal · 4 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 465 | 0.65 | 0.77 | 52 | empty |
| 2 | 225 | 0.52 | 0.76 | 30 | MN, D5M |
| 3 | 197 | 0.51 | 0.77 | 26 | MN, D5M |
| 4 | 68 | 0.30 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- B–A · 1748 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 2IOC · The crystal structure of TREX1 explains the 3' nucleotide specificity and reveals a… · the same entry in another collection · chain B against B, 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 B 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 2IOC · PDBe 2IOC · UniProt Q91XB0
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