MolNFT v1 · #122391 · protein + DNA
Human TDP2 reaction product (5'-phosphorylated DNA)-MG2+ complex
5INO · Tyrosyl-DNA phosphodiesterase 2: “Human TDP2 reaction product (5'-phosphorylated DNA)-MG2+ complex”. X-ray diffraction, 1 ligand (SO4), 1 pocket (best druggability 0.61). MolNFT v1 #122391 on GenesisL1: 3D structure, binding sites…
- PDB
- 5INO
- Type
- protein + DNA
- Length
- 519 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosyl-DNA phosphodiesterase 2; DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
- EC
- 3.1.4.-
- UniProt
- O95551
- Ligands
- SO4
- Pockets
- 1 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 253 | 22% helix, 35% strand | O95551 |
| D, C | DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3') | dna | 9 | — | — |
| B | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 248 | 22% helix, 35% strand | O95551 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 539 | 0.61 | 0.75 | 36 | empty |
Interfaces
5 interfaces between chains.
- A–D · 445 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–C · 445 Ų buried · 8 hydrogen bonds · protein-nucleic
- D–C · 368 Ų buried · 36 hydrogen bonds · nucleic-nucleic
- A–C · 139 Ų buried · 2 hydrogen bonds · protein-nucleic
- D–B · 77 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 5INO · Human Tdp2 reaction product (5'-phosphorylated DNA)-Mg2+ complex · 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 5INO · PDBe 5INO · UniProt O95551
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