MolNFT v1 · #122387 · protein + DNA
Mouse TDP2 reaction product (5'-phosphorylated DNA)-ABASIC/THF-MG2+ complex
5INK · Tyrosyl-DNA phosphodiesterase 2: “Mouse TDP2 reaction product (5'-phosphorylated DNA)-ABASIC/THF-MG2+ complex”. X-ray diffraction, 1 ligand (MG), 1 pocket (best druggability 0.69). MolNFT v1 #122387 on GenesisL1: 3D structure…
- PDB
- 5INK
- Type
- protein + DNA
- Length
- 520 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosyl-DNA phosphodiesterase 2; DNA (5'-D(P*(3DR)P*CP*GP*AP*AP*TP*TP*CP*G)-3')
- EC
- 3.1.4.-
- UniProt
- Q9JJX7
- Ligands
- MG
- Pockets
- 1 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 254 | 25% helix, 36% strand | Q9JJX7 |
| B | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 248 | 22% helix, 36% strand | Q9JJX7 |
| C, D | DNA (5'-D(P*(3DR)P*CP*GP*AP*AP*TP*TP*CP*G)-3') | dna | 9 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, D, B, C
- GOL · Glycerol · additive · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B
- PEG · Di(hydroxyethyl)ether · additive · chains B
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 | 831 | 0.69 | 0.76 | 54 | MG |
Interfaces
6 interfaces between chains.
- A–D · 444 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–C · 381 Ų buried · 9 hydrogen bonds · protein-nucleic
- C–D · 362 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- B–D · 148 Ų buried · 1 hydrogen bond · protein-nucleic
- A–C · 116 Ų buried · 0 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 5INK · Mouse Tdp2 reaction product (5'-phosphorylated DNA)-abasic/THF-Mg2+ complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q9JJX7 · AlphaFold monomer V2.0 prediction for tyrosyl-DNA phosphodiesterase 2 (Q9JJX7) · a predicted model of the same protein · chain A 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 Q9JJX7
- Elsewhere: RCSB PDB 5INK · PDBe 5INK · UniProt Q9JJX7
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