Research workbench
Structure of the L. blandensis dgtpase R37A mutant bound to mn
Analyse Structure of the L. blandensis dgtpase R37A mutant bound to mn in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TU2
- Type
- protein
- Length
- 1,290 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dgtp triphosphohydrolase
- UniProt
- A3XHN1
- Ligands
- MN, SO4
- Pockets
- 12 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 67% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dgtp triphosphohydrolase | protein | 434 | 66% helix, 2% strand | A3XHN1 |
| B | Dgtp triphosphohydrolase | protein | 426 | 67% helix, 2% strand | A3XHN1 |
| C | Dgtp triphosphohydrolase | protein | 430 | 67% helix, 2% strand | A3XHN1 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 667 | 0.71 | 0.78 | 77 | empty |
| 2 | 687 | 0.71 | 0.78 | 79 | empty |
| 3 | 596 | 0.70 | 0.79 | 57 | empty |
| 4 | 910 | 0.70 | 0.76 | 67 | empty |
| 5 | 233 | 0.49 | 0.74 | 37 | empty |
Interfaces
3 interfaces between chains.
- A–B · 691 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 670 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 659 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7TU2 · Structure of the L. blandensis dGTPase R37A mutant bound to Mn · 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 7TU2 · PDBe 7TU2 · UniProt A3XHN1
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