MolNFT v1 · #146559 · protein
Human mitochondrial clpp in complex with ONC201 (TIC10)
6DL7 · ATP-dependent clp protease proteolytic subunit…: “Human mitochondrial clpp in complex with ONC201 (TIC10)”. X-ray diffraction, 1 ligand (ONC), 20 pockets (best druggability 0.71). MolNFT v1 #146559 on GenesisL1: 3D structure…
- PDB
- 6DL7
- Type
- protein
- Length
- 1,244 residues
- Chains
- 7
- 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
- ONC
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 7 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent clp protease proteolytic subunit, mitochondrial (EC 3.4.21.92) | protein | 175 | 45% helix, 18% strand | Q16740 |
| B | ATP-dependent clp protease proteolytic subunit, mitochondrial (EC 3.4.21.92) | protein | 174 | 45% helix, 18% strand | Q16740 |
| C | ATP-dependent clp protease proteolytic subunit, mitochondrial (EC 3.4.21.92) | protein | 178 | 43% helix, 18% strand | Q16740 |
| D | ATP-dependent clp protease proteolytic subunit, mitochondrial (EC 3.4.21.92) | protein | 177 | 45% helix, 18% strand | Q16740 |
| E | ATP-dependent clp protease proteolytic subunit, mitochondrial (EC 3.4.21.92) | protein | 180 | 44% helix, 18% strand | Q16740 |
| F | ATP-dependent clp protease proteolytic subunit, mitochondrial (EC 3.4.21.92) | protein | 179 | 44% helix, 18% strand | Q16740 |
| G | ATP-dependent clp protease proteolytic subunit, mitochondrial (EC 3.4.21.92) | protein | 181 | 43% helix, 18% strand | Q16740 |
Ligands and binding sites
- ONC · 7-benzyl-4-[(2-methylphenyl)methyl]-6,7,8,9-tetrahydroimidazo[1,2-a]pyrido[3,4-e]pyrimidin-5(4H)-one · ligand · 7 copies · chains A, G, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 393 | 0.71 | 0.82 | 49 | empty |
| 2 | 477 | 0.69 | 0.79 | 52 | empty |
| 3 | 233 | 0.61 | 0.81 | 27 | empty |
| 4 | 192 | 0.61 | 0.82 | 24 | ONC |
| 5 | 166 | 0.60 | 0.82 | 23 | ONC |
Interfaces
8 interfaces between chains.
- E–F · 1451 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1448 Ų buried · 10 hydrogen bonds · protein-protein
- F–G · 1440 Ų buried · 13 hydrogen bonds · protein-protein
- A–G · 1424 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 1417 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6DL7 · Human mitochondrial ClpP in complex with ONC201 (TIC10) · the same entry in another collection · chain G against G, TM-score 1.00
- Q16740 · AlphaFold monomer V2.0 prediction for ATP-dependent clp protease proteolytic subunit… · a predicted model of the same protein · chain B against A, TM-score 0.97
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 6DL7 · PDBe 6DL7 · UniProt Q16740
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