Research workbench
CLPP1 from mycobacterium smegmatis
Analyse CLPP1 from mycobacterium smegmatis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PBU
- Type
- protein
- Length
- 1,336 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent clp protease proteolytic subunit
- EC
- 3.4.21.92
- UniProt
- A0R198
- Pockets
- 14 · best druggability 0.60
Structure
x-ray diffraction · 6 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 190 | 46% helix, 18% strand | A0R198 |
| B | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 191 | 46% helix, 18% strand | A0R198 |
| C | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 190 | 46% helix, 18% strand | A0R198 |
| D, F | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 192 | 45% helix, 18% strand | A0R198 |
| E | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 188 | 46% helix, 18% strand | A0R198 |
| G | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 193 | 45% helix, 18% strand | A0R198 |
Ligands and binding sites
- MLI · Malonate ion · additive · 9 copies · chains B, C, D, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 191 | 0.60 | 0.82 | 27 | empty |
| 2 | 181 | 0.58 | 0.82 | 32 | MLI |
| 3 | 221 | 0.52 | 0.77 | 26 | empty |
| 4 | 134 | 0.49 | 0.79 | 36 | empty |
| 5 | 52 | 0.49 | 0.87 | 19 | empty |
Interfaces
7 interfaces between chains.
- F–G · 1715 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 1692 Ų buried · 13 hydrogen bonds · protein-protein
- A–G · 1682 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1678 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1676 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 6PBU · ClpP1 from Mycobacterium smegmatis · the same entry in another collection · 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 A0R198
- Elsewhere: RCSB PDB 6PBU · PDBe 6PBU · UniProt A0R198
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