MolNFT v1 · #188483 · protein
Structure of the L. blandensis dgtpase bound to mn
7TU0 · Dgtp triphosphohydrolase: “Structure of the L. blandensis dgtpase bound to mn”. X-ray diffraction, 2 ligands (MN, SO4), 17 pockets (best druggability 0.72). MolNFT v1 #188483 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7TU0
- Type
- protein
- Length
- 1,292 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dgtp triphosphohydrolase
- UniProt
- A3XHN1
- Ligands
- MN, SO4
- Pockets
- 17 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 66% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dgtp triphosphohydrolase | protein | 430 | 66% helix, 2% strand | A3XHN1 |
| B | Dgtp triphosphohydrolase | protein | 431 | 66% helix, 2% strand | A3XHN1 |
| C | Dgtp triphosphohydrolase | protein | 431 | 66% helix, 2% strand | A3XHN1 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1123 | 0.72 | 0.76 | 93 | empty |
| 2 | 466 | 0.69 | 0.80 | 49 | empty |
| 3 | 446 | 0.68 | 0.80 | 47 | empty |
| 4 | 467 | 0.66 | 0.78 | 49 | empty |
| 5 | 195 | 0.52 | 0.78 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 676 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 637 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 633 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7TU0 · Structure of the L. blandensis dGTPase 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 7TU0 · PDBe 7TU0 · UniProt A3XHN1
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