UniProt Q8IV08
5'-3' exonuclease PLD3 (Q8IV08)
5'-3' exonuclease PLD3 (UniProt Q8IV08), EC 3.1.16.1: 4 experimental structures and 1 predicted model on GenesisL1, 8 ligands bound, 23 pockets. Binding sites, druggability and experiment against prediction (TM-score) in GL1X.
- UniProt
- Q8IV08
- Protein
- 5'-3' exonuclease PLD3
- EC
- 3.1.16.1
- Experimental structures
- 4
- Predicted models
- 1
- Ligands
- 8
- Pockets
- 23 · 5 records with a druggable one
Structures
5 records of Q8IV08 in the MolNFT archive: 4 experimental, 1 predicted.
| Entry | Title | Method | Chains | Ligands | Pockets |
|---|---|---|---|---|---|
| 8Q1K | Structural analysis of PLD3 reveals insights into the mechanism of lysosomal 5'… | x-ray diffraction | A, B | NAG, MAN, BMA, PO4, MN | 4 (best 0.64) |
| 8Q1X | Structural analysis of PLD3 reveals insights into the mechanism of lysosomal 5'… | x-ray diffraction | A, B | NAG, MAN, PST, PO4, MN, SO4 | 6 (best 0.64) |
| 8S86 | human PLD3 homodimer structure | electron microscopy | A, B | — | 6 (best 0.57) |
| 8V5T | Crystal structure of Alzheimers disease phospholipase D3 | x-ray diffraction | A, B | NAG, SO4 | 4 (best 0.61) |
| Q8IV08 | AlphaFold monomer V2.0 prediction for 5'-3' exonuclease PLD3 (Q8IV08) | predicted | A | — | 3 (best 0.59) |
Ligands
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · in 3 records
- MAN · alpha-D-mannopyranose · in 2 records
- MN · Manganese (II) ion · in 2 records
- PO4 · Phosphate ion · in 2 records
- SO4 · Sulfate ion · in 2 records
- BMA · beta-D-mannopyranose · in 1 record
- MG · Magnesium ion · in 1 record
- PST · Thymidine-5'-thiophosphate · in 1 record
Experiment against prediction
- 8V5T chain A against the predicted model Q8IV08: TM-score 0.99, RMSD 0.76 Å
- 8V5T chain B against the predicted model Q8IV08: TM-score 0.99, RMSD 0.78 Å
- 8Q1X chain B against the predicted model Q8IV08: TM-score 0.98, RMSD 0.80 Å
- 8Q1K chain B against the predicted model Q8IV08: TM-score 0.98, RMSD 0.84 Å
- 8Q1X chain A against the predicted model Q8IV08: TM-score 0.98, RMSD 0.78 Å
- 8Q1K chain A against the predicted model Q8IV08: TM-score 0.98, RMSD 0.80 Å
- 8S86 chain A against the predicted model Q8IV08: TM-score 0.98, RMSD 1.13 Å
- 8S86 chain B against the predicted model Q8IV08: TM-score 0.98, RMSD 1.16 Å
Elsewhere
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