Research workbench
Se-met structure of apo- escherichia COLI dgtpase
Analyse Se-met structure of apo- escherichia COLI dgtpase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OI7
- Type
- protein
- Length
- 2,981 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyguanosinetriphosphate triphosphohydrolase
- EC
- 3.1.5.1
- UniProt
- P15723
- Ligands
- MN, SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 63% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxyguanosinetriphosphate triphosphohydrolase (EC 3.1.5.1) | protein | 498 | 63% helix, 2% strand | P15723 |
| B | Deoxyguanosinetriphosphate triphosphohydrolase (EC 3.1.5.1) | protein | 488 | 63% helix, 2% strand | P15723 |
| C | Deoxyguanosinetriphosphate triphosphohydrolase (EC 3.1.5.1) | protein | 497 | 64% helix, 2% strand | P15723 |
| D | Deoxyguanosinetriphosphate triphosphohydrolase (EC 3.1.5.1) | protein | 497 | 63% helix, 2% strand | P15723 |
| E | Deoxyguanosinetriphosphate triphosphohydrolase (EC 3.1.5.1) | protein | 498 | 63% helix, 2% strand | P15723 |
| F | Deoxyguanosinetriphosphate triphosphohydrolase (EC 3.1.5.1) | protein | 503 | 62% helix, 2% strand | P15723 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, C, E, D, 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 | 1059 | 0.83 | 0.84 | 125 | empty |
| 2 | 658 | 0.79 | 0.84 | 92 | empty |
| 3 | 537 | 0.77 | 0.84 | 81 | empty |
| 4 | 516 | 0.76 | 0.84 | 57 | empty |
| 5 | 519 | 0.76 | 0.84 | 61 | empty |
Interfaces
12 interfaces between chains.
- A–F · 2498 Ų buried · 39 hydrogen bonds · protein-protein
- B–D · 2308 Ų buried · 26 hydrogen bonds · protein-protein
- C–E · 2304 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 925 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 883 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 60 modified (engineered).
Compared structures
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 P15723
- Elsewhere: RCSB PDB 6OI7 · PDBe 6OI7 · UniProt P15723
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