Research workbench
Crystal structure of the hclpp Y118A mutant with an activating small molecule
Analyse Crystal structure of the hclpp Y118A mutant with an activating small molecule in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H23
- Type
- protein
- Length
- 2,328 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent clp protease proteolytic subunit, mitochondrial
- EC
- 3.4.21.92
- UniProt
- Q16740
- Ligands
- FJT
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 8 distinct chains · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent clp protease proteolytic subunit, mitochondrial (EC 3.4.21.92) | protein | 165 | 47% helix, 19% strand | Q16740 |
| B | ATP-dependent clp protease proteolytic subunit, mitochondrial (EC 3.4.21.92) | protein | 166 | 47% helix, 20% strand | Q16740 |
| C, E, J, K, L, M | ATP-dependent clp protease proteolytic subunit, mitochondrial (EC 3.4.21.92) | protein | 166 | 46% helix, 20% strand | Q16740 |
| D | ATP-dependent clp protease proteolytic subunit, mitochondrial (EC 3.4.21.92) | protein | 164 | 46% helix, 21% strand | Q16740 |
| F | ATP-dependent clp protease proteolytic subunit, mitochondrial (EC 3.4.21.92) | protein | 166 | 46% helix, 20% strand | Q16740 |
| G | ATP-dependent clp protease proteolytic subunit, mitochondrial (EC 3.4.21.92) | protein | 169 | 46% helix, 20% strand | Q16740 |
| H, I | ATP-dependent clp protease proteolytic subunit, mitochondrial (EC 3.4.21.92) | protein | 167 | 47% helix, 20% strand | Q16740 |
| N | ATP-dependent clp protease proteolytic subunit, mitochondrial (EC 3.4.21.92) | protein | 168 | 46% helix, 20% strand | Q16740 |
Ligands and binding sites
- FJT · ~{N}-(1,3-benzodioxol-5-ylmethyl)-5-[(2-chloranyl-4-fluoranyl-phenyl)methyl]-1,3,4-oxadiazole-2-carboxamide · ligand · 14 copies · chains A, B, C, D, E, F, G, H, N, I, J, K, L, M
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, H, E, K, F, J, 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 | 381 | 0.68 | 0.81 | 42 | FJT |
| 2 | 481 | 0.67 | 0.78 | 54 | EDO |
| 3 | 235 | 0.66 | 0.83 | 25 | FJT |
| 4 | 240 | 0.65 | 0.83 | 30 | FJT |
| 5 | 261 | 0.65 | 0.82 | 26 | FJT |
Interfaces
28 interfaces between chains.
- B–C · 1189 Ų buried · 9 hydrogen bonds · protein-protein
- L–M · 1187 Ų buried · 8 hydrogen bonds · protein-protein
- F–G · 1171 Ų buried · 9 hydrogen bonds · protein-protein
- H–I · 1168 Ų buried · 7 hydrogen bonds · protein-protein
- I–J · 1165 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6H23 · Crystal structure of the hClpP Y118A mutant with an activating small molecule · 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 Q16740
- Elsewhere: RCSB PDB 6H23 · PDBe 6H23 · UniProt Q16740
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