Research workbench
Structure of Thermus thermophilus ClpP in complex with bortezomib
Analyse Structure of Thermus thermophilus ClpP in complex with bortezomib in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HWM
- Type
- protein
- Length
- 1,311 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- Source
- Thermus thermophilus
- Molecule
- ATP-dependent Clp protease proteolytic subunit
- EC
- 3.4.21.92
- UniProt
- Q5SKM8
- Ligands
- BO2
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · resolution 2.7 · 7 distinct chains · 45% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) | protein | 185 | 45% helix, 22% strand | Q5SKM8 |
| B | ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) | protein | 192 | 44% helix, 20% strand | Q5SKM8 |
| C | ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) | protein | 183 | 46% helix, 20% strand | Q5SKM8 |
| D | ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) | protein | 184 | 46% helix, 21% strand | Q5SKM8 |
| E | ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) | protein | 195 | 43% helix, 20% strand | Q5SKM8 |
| F | ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) | protein | 189 | 44% helix, 21% strand | Q5SKM8 |
| G | ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) | protein | 183 | 46% helix, 20% strand | Q5SKM8 |
Ligands and binding sites
- BO2 · N-[(1R)-1-(dihydroxyboryl)-3-methylbutyl]-N-(pyrazin-2-ylcarbonyl)-L-phenylalaninamide · ligand · 7 copies · chains A, B, C, D, E, F, G
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 475 | 0.68 | 0.79 | 55 | empty |
| 2 | 338 | 0.65 | 0.80 | 46 | empty |
| 3 | 289 | 0.59 | 0.78 | 42 | BO2 |
| 4 | 283 | 0.59 | 0.78 | 38 | BO2 |
| 5 | 270 | 0.59 | 0.78 | 37 | BO2 |
Interfaces
7 interfaces between chains.
- E–F · 1603 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1545 Ų buried · 17 hydrogen bonds · protein-protein
- A–G · 1542 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1530 Ų buried · 14 hydrogen bonds · protein-protein
- F–G · 1525 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 covalent (covalent ligand).
Compared structures
- 6HWM · Structure of thermus thermophilus clpp in complex with bortezomib · the same entry in another collection · chain G against G, TM-score 1.00
- Q5SKM8 · AlphaFold monomer V2.0 prediction for ATP-dependent clp protease proteolytic subunit… · a predicted model of the same protein · chain G against A, TM-score 0.99
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 Q5SKM8
- Elsewhere: RCSB PDB 6HWM · PDBe 6HWM · UniProt Q5SKM8
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