Research workbench
Structure of the L. blandensis dgtpase bound to datp
Analyse Structure of the L. blandensis dgtpase bound to datp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TU6
- Type
- protein
- Length
- 2,580 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dgtp triphosphohydrolase
- EC
- 3.1.5.1
- UniProt
- A3XHN1
- Ligands
- DTP, MG
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 1 distinct chain · 62% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Dgtp triphosphohydrolase (EC 3.1.5.1) | protein | 430 | 62% helix, 1% strand | A3XHN1 |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 12 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 334 | 0.78 | 0.89 | 45 | empty |
| 2 | 318 | 0.78 | 0.89 | 47 | empty |
| 3 | 355 | 0.78 | 0.88 | 48 | empty |
| 4 | 906 | 0.74 | 0.78 | 105 | empty |
| 5 | 1100 | 0.73 | 0.76 | 84 | DTP |
Interfaces
9 interfaces between chains.
- C–D · 1742 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 1737 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1730 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 634 Ų buried · 1 hydrogen bond · protein-protein
- B–F · 633 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7TU6 · Structure of the L. blandensis dGTPase bound to dATP · the same entry in another collection · chain A against A, 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 A3XHN1
- Elsewhere: RCSB PDB 7TU6 · PDBe 7TU6 · UniProt A3XHN1
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