Research workbench
Structure of PROTEASE1 from pyrococcus horikoshii in space group 19 with a hexamer in the asymmetric unit
Analyse Structure of PROTEASE1 from pyrococcus horikoshii in space group 19 with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QO8
- Type
- protein
- Length
- 996 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deglycase PH1704
- EC
- 3.5.1.124, 3.4.22.-
- UniProt
- O59413
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Deglycase PH1704 (EC 3.5.1.124, 3.4.22.-) | protein | 166 | 39% helix, 26% strand | O59413 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 236 | 0.54 | 0.77 | 36 | empty |
| 2 | 262 | 0.54 | 0.76 | 32 | empty |
| 3 | 174 | 0.49 | 0.77 | 34 | empty |
| 4 | 105 | 0.38 | 0.75 | 17 | empty |
| 5 | 92 | 0.38 | 0.75 | 15 | empty |
Interfaces
6 interfaces between chains.
- D–E · 883 Ų buried · 23 hydrogen bonds · protein-protein
- A–F · 882 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 864 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 725 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 718 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 7QO8 · Structure of Protease1 from Pyrococcus horikoshii in space group 19 with a hexamer in the… · the same entry in another collection · chain C against C, TM-score 1.00
- O59413 · AlphaFold monomer V2.0 prediction for deglycase PH1704 (O59413) · a predicted model of the same protein · 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 O59413
- Elsewhere: RCSB PDB 7QO8 · PDBe 7QO8 · UniProt O59413
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