UniProt Q9JJX7
Tyrosyl-DNA phosphodiesterase 2 (Q9JJX7)
Tyrosyl-DNA phosphodiesterase 2 (UniProt Q9JJX7), EC 3.1.4.-: 32 experimental structures and 1 predicted model on GenesisL1, 8 ligands bound, 24 pockets. Binding sites, druggability and experiment against prediction (TM-score) in…
- UniProt
- Q9JJX7
- Protein
- Tyrosyl-DNA phosphodiesterase 2
- EC
- 3.1.4.-
- Experimental structures
- 32
- Predicted models
- 1
- Ligands
- 8
- Pockets
- 24 · 3 records with a druggable one
Structures
33 records of Q9JJX7 in the MolNFT archive: 32 experimental, 1 predicted.
| Entry | Title | Method | Chains | Ligands | Pockets |
|---|---|---|---|---|---|
| 4GYZ | Mus Musculus Tdp2 Bound to dAMP and Mg2+ | x-ray diffraction | A, B, C, D, E, F, G, H, I | — | — |
| 4GYZ | Mus musculus TDP2 bound to damp and MG2+ | x-ray diffraction | A, B, C, D, E, F, G, H, I | — | — |
| 4GZ0 | Mus Musculus Tdp2-DNA Substrate Analog (5'-6-aminohexanol) Complex | x-ray diffraction | A, B, E, K, G, I | — | — |
| 4GZ0 | Mus musculus TDP2-DNA substrate analog (5'-6-aminohexanol) complex | x-ray diffraction | A, B, E, K, G, I | — | — |
| 4GZ1 | Mus Musculus Tdp2 reaction product (5'-phosphorylated DNA)-Mg2+ complex at 1.5 Angstroms resolution | x-ray diffraction | A, B | — | — |
| 4GZ1 | Mus musculus TDP2 reaction product (5'-phosphorylated DNA)-MG2+ complex at 1.5 ångströms resolution | x-ray diffraction | A, B | — | — |
| 4GZ2 | Mus Musculus Tdp2 excluded ssDNA complex | x-ray diffraction | A, B | — | — |
| 4GZ2 | Mus musculus TDP2 excluded ssdna complex | x-ray diffraction | A, B | — | — |
| 4PUQ | Mus Musculus Tdp2 reaction product complex with 5'-phosphorylated RNA/DNA, glycerol, and Mg2+ | x-ray diffraction | A, B | — | — |
| 4PUQ | Mus musculus TDP2 reaction product complex with 5'-phosphorylated RNA/DNA, glycerol, and MG2+ | x-ray diffraction | A, B | — | — |
| 5HT2 | Mouse Tdp2 reaction product (5'-phosphorylated DNA)-Mg2+ complex with 1-N6-etheno-adenine | x-ray diffraction | A, B | MG | 1 (best 0.68) |
| 5HT2 | Mouse TDP2 reaction product (5'-phosphorylated DNA)-MG2+ complex with 1-N6-etheno-adenine | x-ray diffraction | A, B | — | — |
| 5INK | Mouse Tdp2 reaction product (5'-phosphorylated DNA)-abasic/THF-Mg2+ complex | x-ray diffraction | A, B | MG | — |
| 5INK | Mouse TDP2 reaction product (5'-phosphorylated DNA)-ABASIC/THF-MG2+ complex | x-ray diffraction | A, B | — | — |
| 5INL | Mouse Tdp2 reaction product (5'-phosphorylated DNA)-Mg2+ complex with deoxyadenosine | x-ray diffraction | A, B | MG | — |
| 5INL | Mouse TDP2 reaction product (5'-phosphorylated DNA)-MG2+ complex with deoxyadenosine | x-ray diffraction | A, B | — | — |
| 5INM | Mouse Tdp2 protein, apo state with variable DNA-binding grasp conformations | x-ray diffraction | A, B, C, D, E | MG, SO4 | — |
| 5INM | Mouse TDP2 protein, apo state with variable DNA-binding grasp conformations | x-ray diffraction | A, B, C, D, E | — | — |
| 5INN | Mouse Tdp2 D358N protein, apo state with increased disorder amongst variable DNA-binding grasp… | x-ray diffraction | A, B, C, D, E | SO4, CL | — |
| 5INN | Mouse TDP2 D358N protein, apo state with increased disorder amongst variable DNA-binding grasp… | x-ray diffraction | A, B, C, D, E | — | — |
| 5INP | Mouse Tdp2 reaction product (5'-phosphorylated DNA)-Mn2+ complex | x-ray diffraction | A, B | MN | 1 (best 0.67) |
| 5INP | Mouse TDP2 reaction product (5'-phosphorylated DNA)-MN2+ complex | x-ray diffraction | A, B | — | — |
| 5INQ | Mouse Tdp2 reaction product (5'-phosphorylated DNA)-Ca2+ complex | x-ray diffraction | A, B | CA | — |
| 5INQ | Mouse TDP2 reaction product (5'-phosphorylated DNA)-CA2+ complex | x-ray diffraction | A, B | — | — |
| 5J3Z | Crystal structure of m2hTDP2-CAT in complex with a small molecule inhibitor | x-ray diffraction | A, B | 6FQ, MG | — |
| 5J3Z | Crystal structure of M2HTDP2-cat in complex with a small molecule inhibitor | x-ray diffraction | A, B | — | — |
| 5J42 | Crystal structure of m2hTDP2-CAT in complex with a small molecule inhibitor | x-ray diffraction | A, B | 6FV, MN | — |
| 5J42 | Crystal structure of M2HTDP2-cat in complex with a small molecule inhibitor | x-ray diffraction | A, B | — | — |
| 5TVP | SUMO2 bound to Mouse Tdp2 catalytic domain with a 5'-phosphorylated DNA ternary complex | x-ray diffraction | I, O, E, G, B, A, K, M | PO4, CL | 20 (best 0.79) |
| 5TVP | SUMO2 bound to mouse TDP2 catalytic domain with a 5'-phosphorylated DNA ternary complex | x-ray diffraction | I, O, E, G, B, A, K, M | PO4, CL | — |
| 5TVQ | Mouse Tdp2 catalytic domain bound to SUMO2 | x-ray diffraction | A | CA | — |
| 5TVQ | Mouse TDP2 catalytic domain bound to SUMO2 | x-ray diffraction | A | CA | — |
| Q9JJX7 | AlphaFold monomer V2.0 prediction for tyrosyl-DNA phosphodiesterase 2 (Q9JJX7) | predicted | A | — | 2 (best 0.34) |
Ligands
- MG · Magnesium ion · in 5 records
- CA · Calcium ion · in 3 records
- CL · Chloride ion · in 3 records
- MN · Manganese (II) ion · in 2 records
- PO4 · Phosphate ion · in 2 records
- SO4 · Sulfate ion · in 2 records
- 6FQ · 2,4-dioxo-10-[3-(1H-tetrazol-5-yl)phenyl]-2,3,4,10-tetrahydropyrimido[4,5-b]quinoline-8-carbonitrile · in 1 record
- 6FV · 10-(4-hydroxyphenyl)-2,4-dioxo-2,3,4,10-tetrahydropyrimido[4,5-b]quinoline-8-carbonitrile · in 1 record
Experiment against prediction
- 5TVP chain G against the predicted model Q9JJX7: TM-score 1.00, RMSD 0.39 Å
- 5J42 chain B against the predicted model Q9JJX7: TM-score 0.99, RMSD 0.44 Å
- 5J42 chain B against the predicted model Q9JJX7: TM-score 0.99, RMSD 0.44 Å
- 5INM chain C against the predicted model Q9JJX7: TM-score 0.99, RMSD 0.44 Å
- 5INM chain C against the predicted model Q9JJX7: TM-score 0.99, RMSD 0.44 Å
- 5TVP chain E against the predicted model Q9JJX7: TM-score 0.99, RMSD 0.44 Å
- 5TVP chain E against the predicted model Q9JJX7: TM-score 0.99, RMSD 0.44 Å
- 5INK chain A against the predicted model Q9JJX7: TM-score 0.99, RMSD 0.51 Å
- 5INK chain A against the predicted model Q9JJX7: TM-score 0.99, RMSD 0.51 Å
- 4GZ0 chain K against the predicted model Q9JJX7: TM-score 0.99, RMSD 0.46 Å
Elsewhere
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