Research workbench
TREX1 3' exonuclease V201D aicardi-goutieres syndrome mutant
Analyse TREX1 3' exonuclease V201D aicardi-goutieres syndrome mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MXM
- Type
- protein + DNA
- Length
- 457 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Three prime repair exonuclease 1; DNA (5'-D(*GP*AP*CP*G)-3')
- EC
- 3.1.11.2
- UniProt
- Q91XB0
- Ligands
- CA, IOD
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 3 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 | 223 | 40% helix, 16% strand | Q91XB0 |
| A | Three prime repair exonuclease 1 (EC 3.1.11.2) | protein | 226 | 40% helix, 16% strand | Q91XB0 |
| C, D | DNA (5'-D(*GP*AP*CP*G)-3') | dna | 4 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains B, D, A, C
- IOD · Iodide ion · ion · 12 copies · chains B, A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 449 | 0.61 | 0.76 | 48 | empty |
| 2 | 95 | 0.38 | 0.76 | 25 | IOD |
| 3 | 60 | 0.38 | 0.80 | 16 | empty |
| 4 | 53 | 0.27 | 0.74 | 17 | IOD |
Interfaces
3 interfaces between chains.
- B–A · 1774 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 588 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–D · 579 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 3MXM · TREX1 3' Exonuclease V201D Aicardi-Goutieres Syndrome Mutant · 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 1.00
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 3MXM · PDBe 3MXM · UniProt Q91XB0
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