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The structure of thermococcus thioreducens' inorganic pyrophosphatase bound to sulfate
Analyse The structure of thermococcus thioreducens' inorganic pyrophosphatase bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3R6E
- Type
- protein
- Length
- 1,040 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tt-ippase
- Ligands
- SO4, NH4
- Pockets
- 14 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 26% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, F | Tt-ippase | protein | 175 | 26% helix, 34% strand | — |
| B | Tt-ippase | protein | 172 | 26% helix, 31% strand | — |
| D | Tt-ippase | protein | 173 | 26% helix, 32% strand | — |
| E | Tt-ippase | protein | 170 | 26% helix, 28% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 440 | 0.79 | 0.87 | 37 | empty |
| 2 | 434 | 0.79 | 0.87 | 33 | empty |
| 3 | 298 | 0.74 | 0.87 | 41 | empty |
| 4 | 291 | 0.74 | 0.86 | 43 | empty |
| 5 | 287 | 0.74 | 0.86 | 43 | empty |
Interfaces
12 interfaces between chains.
- A–E · 829 Ų buried · 10 hydrogen bonds · protein-protein
- C–F · 825 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 823 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 820 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 817 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified (engineered).
Compared structures
- 3R6E · The structure of Thermococcus thioreducens' inorganic pyrophosphatase bound to sulfate · 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
- Elsewhere: RCSB PDB 3R6E · PDBe 3R6E
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