Research workbench
Crystal structure of dntp triphosphohydrolase from thermus thermophilus HB8, which is homologous to dgtp triphosphohydrolase
Analyse Crystal structure of dntp triphosphohydrolase from thermus thermophilus HB8… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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