Research workbench
Crystal structure of a novel intracellular protease from pyrococcus horikoshii at 2 a resolution
Analyse Crystal structure of a novel intracellular protease from pyrococcus horikoshii… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1G2I
- Type
- protein
- Length
- 498 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease I
- EC
- 3.2.-.-
- UniProt
- O59413
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Protease I (EC 3.2.-.-) | protein | 166 | 40% helix, 25% strand | O59413 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 275 | 0.59 | 0.78 | 34 | empty |
| 2 | 132 | 0.44 | 0.76 | 18 | empty |
| 3 | 100 | 0.43 | 0.78 | 17 | empty |
Interfaces
2 interfaces between chains.
- A–B · 874 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 788 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 1G2I · Crystal structure of a novel intracellular protease from pyrococcus horikoshii at 2 a… · 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 B 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 1G2I · PDBe 1G2I · UniProt O59413
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