MolNFT v1 · #34762 · protein
Crystal structure of dntp triphosphohydrolase from thermus thermophilus HB8, which is homologous to dgtp triphosphohydrolase
2DQB · Deoxyguanosinetriphosphate triphosphohydrolase, putative: “Crystal structure of dntp triphosphohydrolase from thermus thermophilus HB8, which is homologous to dgtp…”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability…
- PDB
- 2DQB
- Type
- protein
- Length
- 2,160 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyguanosinetriphosphate triphosphohydrolase, putative
- EC
- 3.1.5.1
- UniProt
- Q5SL81
- Ligands
- MG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 6 distinct chains · 65% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxyguanosinetriphosphate triphosphohydrolase, putative (EC 3.1.5.1) | protein | 363 | 66% helix, 1% strand | Q5SL81 |
| B | Deoxyguanosinetriphosphate triphosphohydrolase, putative (EC 3.1.5.1) | protein | 350 | 65% helix, 1% strand | Q5SL81 |
| C | Deoxyguanosinetriphosphate triphosphohydrolase, putative (EC 3.1.5.1) | protein | 364 | 67% helix, 2% strand | Q5SL81 |
| D | Deoxyguanosinetriphosphate triphosphohydrolase, putative (EC 3.1.5.1) | protein | 361 | 65% helix, 2% strand | Q5SL81 |
| E | Deoxyguanosinetriphosphate triphosphohydrolase, putative (EC 3.1.5.1) | protein | 360 | 63% helix, 1% strand | Q5SL81 |
| F | Deoxyguanosinetriphosphate triphosphohydrolase, putative (EC 3.1.5.1) | protein | 362 | 65% helix, 2% strand | Q5SL81 |
Ligands and binding sites
- 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 454 | 0.87 | 0.95 | 35 | empty |
| 2 | 315 | 0.86 | 0.96 | 29 | empty |
| 3 | 312 | 0.84 | 0.94 | 32 | empty |
| 4 | 733 | 0.83 | 0.87 | 97 | empty |
| 5 | 877 | 0.79 | 0.82 | 88 | empty |
Interfaces
10 interfaces between chains.
- C–F · 2570 Ų buried · 58 hydrogen bonds · protein-protein
- A–D · 2529 Ų buried · 59 hydrogen bonds · protein-protein
- B–E · 2401 Ų buried · 48 hydrogen bonds · protein-protein
- E–F · 648 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 645 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 2DQB · Crystal structure of dNTP triphosphohydrolase from Thermus thermophilus HB8, which is… · 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 Q5SL81
- Elsewhere: RCSB PDB 2DQB · PDBe 2DQB · UniProt Q5SL81
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