MolNFT v1 · #93322 · protein
Mus musculus TDP2 bound to damp and MG2+
4GYZ · Tyrosyl-DNA phosphodiesterase 2: “Mus musculus TDP2 bound to damp and MG2+”. X-ray diffraction, 4 ligands (D5M, MG, CL), 20 pockets (best druggability 0.83). MolNFT v1 #93322 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4GYZ
- Type
- protein
- Length
- 2,207 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosyl-DNA phosphodiesterase 2
- EC
- 3.1.4.-
- UniProt
- Q9JJX7
- Ligands
- D5M, MG, CL, PO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 9 distinct chains · 22% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 246 | 22% helix, 37% strand | Q9JJX7 |
| B | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 249 | 20% helix, 37% strand | Q9JJX7 |
| C | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 248 | 23% helix, 37% strand | Q9JJX7 |
| D | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 238 | 23% helix, 38% strand | Q9JJX7 |
| E | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 249 | 22% helix, 36% strand | Q9JJX7 |
| F | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 244 | 20% helix, 36% strand | Q9JJX7 |
| G | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 243 | 21% helix, 36% strand | Q9JJX7 |
| H | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 244 | 23% helix, 37% strand | Q9JJX7 |
| I | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 246 | 22% helix, 35% strand | Q9JJX7 |
Ligands and binding sites
- D5M · 2'-deoxyadenosine-5'-monophosphate · ligand · 6 copies · chains A, B, C, D, I, E, H
- MG · Magnesium ion · metal · 9 copies · chains A, B, C, D, E, F, G, H, I
- CL · Chloride ion · ion · 3 copies · chains C, D, I
- PO4 · Phosphate ion · ion · chains F
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 | 647 | 0.83 | 0.87 | 51 | D5M, MG |
| 2 | 933 | 0.80 | 0.82 | 102 | empty |
| 3 | 948 | 0.75 | 0.78 | 68 | PO4, MG |
| 4 | 759 | 0.72 | 0.78 | 60 | D5M, MG |
| 5 | 776 | 0.71 | 0.77 | 82 | empty |
Interfaces
13 interfaces between chains.
- E–G · 818 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 736 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 562 Ų buried · 7 hydrogen bonds · protein-protein
- A–F · 525 Ų buried · 10 hydrogen bonds · protein-protein
- D–I · 499 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
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 4GYZ · PDBe 4GYZ · UniProt Q9JJX7
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