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Crystal structure of protease 1 from pyrococcus horikoshii co- cystallized in presence of 10 mm tb-XO4 and ammonium sulfate.
Analyse Crystal structure of protease 1 from pyrococcus horikoshii co- cystallized in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6F2F
- Type
- protein
- Length
- 498 residues
- Chains
- 3
- 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
- 7MT, 2HA, TB, SO4
- Pockets
- 2 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Deglycase PH1704 (EC 3.5.1.124, 3.4.22.-) | protein | 166 | 39% helix, 25% strand | O59413 |
Ligands and binding sites
- 7MT · Tb-Xo4 · ligand · 3 copies · chains A, B, C
- 2HA · Dihydroxyacetone · ligand · chains C
- TB · Terbium(iii) ion · metal
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 329 | 0.61 | 0.78 | 41 | SO4 |
| 2 | 100 | 0.39 | 0.75 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 881 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 719 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6F2F · Crystal structure of Protease 1 from Pyrococcus Horikoshii co-cystallized in presence of… · the same entry in another collection · chain A against A, 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 6F2F · PDBe 6F2F · UniProt O59413
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