MolNFT v1 · #135321 · protein + DNA
SUMO2 bound to mouse TDP2 catalytic domain with a 5'-phosphorylated DNA ternary complex
5TVP · Tyrosyl-DNA phosphodiesterase 2: “SUMO2 bound to mouse TDP2 catalytic domain with a 5'-phosphorylated DNA ternary complex”. X-ray diffraction, 2 ligands (PO4, CL), 20 pockets (best druggability 0.79). MolNFT v1 #135321 on GenesisL1…
- PDB
- 5TVP
- Type
- protein + DNA
- Length
- 2,147 residues
- Chains
- 17
- 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'); Small…
- EC
- 3.1.4.-
- UniProt
- Q9JJX7, P61957
- Ligands
- PO4, CL
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 22% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I, O, G, A, K | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 249 | 22% helix, 37% strand | Q9JJX7 |
| J, P, F, H, C, D, L, N | DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3') | dna | 9 | — | — |
| Q | Small ubiquitin-related modifier 2 | protein | 76 | 14% helix, 36% strand | P61957 |
| E, M | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 250 | 23% helix, 36% strand | Q9JJX7 |
| B | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 254 | 23% helix, 37% strand | Q9JJX7 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 9 copies · chains I, O, E, G, B, A, K, M
- CL · Chloride ion · ion · 3 copies · chains E, K, B, M
- EDO · 1,2-ethanediol · additive · 13 copies · chains I, O, G, B, A, E, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1058 | 0.79 | 0.80 | 104 | empty |
| 2 | 1073 | 0.75 | 0.78 | 62 | empty |
| 3 | 855 | 0.71 | 0.77 | 59 | empty |
| 4 | 781 | 0.70 | 0.77 | 56 | empty |
| 5 | 710 | 0.67 | 0.76 | 56 | empty |
Interfaces
29 interfaces between chains.
- Q–B · 832 Ų buried · 19 hydrogen bonds · protein-protein
- E–K · 652 Ų buried · 12 hydrogen bonds · protein-protein
- M–N · 456 Ų buried · 7 hydrogen bonds · protein-nucleic
- I–J · 449 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–D · 447 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 5TVP · SUMO2 bound to Mouse Tdp2 catalytic domain with a 5'-phosphorylated DNA ternary complex · the same entry in another collection · chain N against N, 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
- Every structure of UniProt P61957
- Elsewhere: RCSB PDB 5TVP · PDBe 5TVP · UniProt Q9JJX7 · UniProt P61957
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