Research workbench
Structure of the L. blandensis dgtpase H125A mutant bound to dgtp
Analyse Structure of the L. blandensis dgtpase H125A mutant bound to dgtp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TU7
- Type
- protein
- Length
- 2,586 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, MG
- Pockets
- 20 · best druggability 0.75
Structure
electron microscopy · 1 distinct chain · 64% 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 | 431 | 64% helix, 1% strand | A3XHN1 |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 18 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 | 904 | 0.75 | 0.79 | 98 | empty |
| 2 | 874 | 0.74 | 0.78 | 90 | empty |
| 3 | 700 | 0.72 | 0.78 | 81 | DGT, MG |
| 4 | 669 | 0.70 | 0.78 | 61 | empty |
| 5 | 676 | 0.70 | 0.77 | 62 | empty |
Interfaces
9 interfaces between chains.
- C–D · 1556 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 1553 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1552 Ų buried · 9 hydrogen bonds · protein-protein
- C–E · 621 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 619 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7TU7 · Structure of the L. blandensis dGTPase H125A mutant bound to dGTP · 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 7TU7 · PDBe 7TU7 · UniProt A3XHN1
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