MolNFT v1 · #142430 · protein
Structure of TREX2 in complex with a nucleotide (dcmp)
6A46 · Three prime repair exonuclease 2: “Structure of TREX2 in complex with a nucleotide (dcmp)”. X-ray diffraction, 3 ligands (DCM, MG, CA), 5 pockets (best druggability 0.57). MolNFT v1 #142430 on GenesisL1: 3D structure, binding sites…
- PDB
- 6A46
- Type
- protein
- Length
- 436 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Three prime repair exonuclease 2
- EC
- 3.1.11.2
- UniProt
- Q9R1A9
- Ligands
- DCM, MG, CA
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Three prime repair exonuclease 2 (EC 3.1.11.2) | protein | 223 | 43% helix, 17% strand | Q9R1A9 |
| B | Three prime repair exonuclease 2 (EC 3.1.11.2) | protein | 213 | 42% helix, 19% strand | Q9R1A9 |
Ligands and binding sites
- DCM · 2'-deoxycytidine-5'-monophosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- CA · Calcium ion · metal · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 330 | 0.57 | 0.76 | 31 | empty |
| 2 | 257 | 0.57 | 0.78 | 28 | MG, DCM, CA |
| 3 | 251 | 0.55 | 0.77 | 26 | DCM, MG |
| 4 | 58 | 0.30 | 0.75 | 17 | empty |
| 5 | 51 | 0.30 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1533 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
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 Q9R1A9
- Elsewhere: RCSB PDB 6A46 · PDBe 6A46 · UniProt Q9R1A9
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