MolNFT v1 · #122910 · protein
Crystal structure of the catalytic domain of human tyrosyl DNA phosphodiesterase 2
5J3P · Tyrosyl-DNA phosphodiesterase 2: “Crystal structure of the catalytic domain of human tyrosyl DNA phosphodiesterase 2”. X-ray diffraction, 1 ligand (MG), 4 pockets (best druggability 0.60). MolNFT v1 #122910 on GenesisL1: 3D…
- PDB
- 5J3P
- Type
- protein
- Length
- 475 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosyl-DNA phosphodiesterase 2
- EC
- 3.1.4.-
- UniProt
- O95551
- Ligands
- MG
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 246 | 20% helix, 37% strand | O95551 |
| B | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 229 | 19% helix, 37% strand | O95551 |
Ligands and binding sites
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 | 305 | 0.60 | 0.78 | 32 | empty |
| 2 | 304 | 0.58 | 0.77 | 45 | MG, GOL |
| 3 | 101 | 0.53 | 0.83 | 22 | empty |
| 4 | 74 | 0.34 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 690 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5J3P · Crystal structure of the catalytic domain of human tyrosyl DNA phosphodiesterase 2 · the same entry in another collection · chain A against A, TM-score 1.00
- O95551 · AlphaFold monomer V2.0 prediction for tyrosyl-DNA phosphodiesterase 2 (O95551) · 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 O95551
- Elsewhere: RCSB PDB 5J3P · PDBe 5J3P · UniProt O95551
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