Research workbench
Mus musculus TDP2-DNA substrate analog (5'-6-aminohexanol) complex
Analyse Mus musculus TDP2-DNA substrate analog (5'-6-aminohexanol) complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GZ0
- Type
- protein + DNA
- Length
- 1,552 residues
- Chains
- 12
- 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
- Q9JJX7
- Ligands
- 6AH
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, I | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 250 | 23% helix, 36% strand | Q9JJX7 |
| C, D, F, L, H, J | DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3') | dna | 9 | — | — |
| K, G | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 249 | 23% helix, 37% strand | Q9JJX7 |
Ligands and binding sites
- 6AH · 6-aminohexan-1-ol · ligand · 6 copies · chains B, C, J, A, D, H, E, F, L, K, G, I
- EDO · 1,2-ethanediol · additive · 113 copies · chains A, H, B, G, J, E, D, F, K, I, C
- ACT · Acetate ion · additive · 22 copies · chains A, B, G, E, K, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1045 | 0.77 | 0.79 | 63 | 6AH, EDO |
| 2 | 1075 | 0.76 | 0.79 | 64 | EDO, 6AH |
| 3 | 1034 | 0.73 | 0.77 | 60 | EDO, 6AH |
| 4 | 391 | 0.68 | 0.80 | 42 | EDO, ACT |
| 5 | 82 | 0.47 | 0.82 | 18 | EDO |
Interfaces
20 interfaces between chains.
- A–D · 454 Ų buried · 9 hydrogen bonds · protein-nucleic
- B–C · 450 Ų buried · 10 hydrogen bonds · protein-nucleic
- I–J · 444 Ų buried · 7 hydrogen bonds · protein-nucleic
- E–F · 442 Ų buried · 12 hydrogen bonds · protein-nucleic
- K–L · 436 Ų buried · 9 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 4GZ0 · Mus Musculus Tdp2-DNA Substrate Analog (5'-6-aminohexanol) Complex · the same entry in another collection · chain J against J, TM-score 1.00
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 4GZ0 · PDBe 4GZ0 · UniProt Q9JJX7
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