Research workbench
Crystal structure of the Protease 1 (E29A,E60A,E80A) from Pyrococcus horikoshii co-crystallized with Tb-Xo4.
Analyse Crystal structure of the Protease 1 (E29A,E60A,E80A) 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
- 6HF6
- Type
- protein
- Length
- 498 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2
- Source
- Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139…
- Molecule
- Deglycase PH1704
- EC
- 3.5.1.124, 3.4.22.-
- UniProt
- O59413
- Ligands
- 7MT, TB
- Pockets
- 2 · best druggability 0.61
Structure
x-ray diffraction · resolution 2 · 1 distinct chain · 40% 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 | 40% helix, 25% strand | O59413 |
Ligands and binding sites
- 7MT · Tb-Xo4 · ligand · 3 copies · chains A, B, C
- TB · Terbium(iii) ion · metal · 4 copies · chains A, B, C
- MLI · Malonate ion · additive · 3 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 | 314 | 0.61 | 0.78 | 42 | TB |
| 2 | 97 | 0.38 | 0.75 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 888 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 740 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6HF6 · Crystal structure of the protease 1 (E29A,E60A,E80A) from pyrococcus horikoshii… · 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 6HF6 · PDBe 6HF6 · UniProt O59413
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