Research workbench
CLPP
Analyse CLPP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YG6
- Type
- protein
- Length
- 2,618 residues
- Chains
- 14
- 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
- P0A6G7
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 8 distinct chains · 45% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E, F | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 193 | 43% helix, 24% strand | P0A6G7 |
| B, G | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 192 | 43% helix, 25% strand | P0A6G7 |
| C | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 189 | 44% helix, 23% strand | P0A6G7 |
| H | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 186 | 45% helix, 24% strand | P0A6G7 |
| I, J | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 184 | 45% helix, 24% strand | P0A6G7 |
| K | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 178 | 47% helix, 25% strand | P0A6G7 |
| L, M | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 182 | 46% helix, 24% strand | P0A6G7 |
| N | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 177 | 47% helix, 25% strand | P0A6G7 |
Ligands and binding sites
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 14 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 825 | 0.81 | 0.84 | 81 | empty |
| 2 | 849 | 0.79 | 0.82 | 94 | MPD |
| 3 | 832 | 0.79 | 0.82 | 90 | empty |
| 4 | 817 | 0.78 | 0.81 | 99 | MPD |
| 5 | 797 | 0.78 | 0.81 | 89 | MPD |
Interfaces
42 interfaces between chains.
- A–G · 1980 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1882 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1882 Ų buried · 25 hydrogen bonds · protein-protein
- H–I · 1879 Ų buried · 34 hydrogen bonds · protein-protein
- F–G · 1866 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 1YG6 · ClpP · the same entry in another collection · chain K against K, 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 P0A6G7
- Elsewhere: RCSB PDB 1YG6 · PDBe 1YG6 · UniProt P0A6G7
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