Research workbench
Structure of the L. blandensis dgtpase H125A mutant bound to dgtp and datp
Analyse Structure of the L. blandensis dgtpase H125A mutant bound to dgtp and datp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TU8
- Type
- protein
- Length
- 2,604 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
- DGT, DTP, MG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 1 distinct chain · 65% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Dgtp triphosphohydrolase (EC 3.1.5.1) | protein | 434 | 65% helix, 2% strand | A3XHN1 |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 12 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 | 363 | 0.82 | 0.91 | 44 | empty |
| 2 | 373 | 0.81 | 0.90 | 43 | empty |
| 3 | 378 | 0.80 | 0.89 | 42 | empty |
| 4 | 89 | 0.76 | 0.97 | 20 | empty |
| 5 | 114 | 0.73 | 0.93 | 27 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1809 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 1806 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1802 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 617 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 615 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7TU8 · Structure of the L. blandensis dGTPase H125A mutant bound to dGTP and 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 7TU8 · PDBe 7TU8 · UniProt A3XHN1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.