MolNFT v1 · #22786 · protein
Crystallography and mutagenesis point to an essential role for the N- terminus of human mitochondrial clpp
1TG6 · Putative ATP-dependent clp protease proteolytic subunit: “Crystallography and mutagenesis point to an essential role for the N- terminus of human mitochondrial clpp”. X-ray diffraction, 1 ligand (FME), 20 pockets (best druggability…
- PDB
- 1TG6
- Type
- protein
- Length
- 1,311 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative ATP-dependent clp protease proteolytic subunit
- EC
- 3.4.21.92
- UniProt
- Q16740
- Ligands
- FME
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 45% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Putative ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 184 | 46% helix, 21% strand | Q16740 |
| B, C | Putative ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 183 | 46% helix, 21% strand | Q16740 |
| E | Putative ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 196 | 43% helix, 21% strand | Q16740 |
| F | Putative ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 187 | 45% helix, 19% strand | Q16740 |
| G | Putative ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 194 | 43% helix, 22% strand | Q16740 |
Ligands and binding sites
- FME · N-formylmethionine · ligand · 7 copies · chains A, B, C, D, E, F, G
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, G, B, C, D, E, F
- DIO · 1,4-diethylene dioxide · additive · 6 copies · chains A, G, B, C, D, E, F
- GOL · Glycerol · additive · 6 copies · chains A, B, C, D, E, F, 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1002 | 0.77 | 0.79 | 113 | empty |
| 2 | 385 | 0.73 | 0.84 | 64 | empty |
| 3 | 200 | 0.66 | 0.84 | 29 | DIO, EDO |
| 4 | 239 | 0.65 | 0.83 | 41 | EDO, DIO |
| 5 | 172 | 0.64 | 0.85 | 29 | EDO |
Interfaces
7 interfaces between chains.
- E–F · 1672 Ų buried · 20 hydrogen bonds · protein-protein
- F–G · 1664 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 1565 Ų buried · 15 hydrogen bonds · protein-protein
- A–G · 1547 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1497 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 1TG6 · Crystallography and mutagenesis point to an essential role for the N-terminus of human… · the same entry in another collection · chain F against F, 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 C 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 Q16740
- Elsewhere: RCSB PDB 1TG6 · PDBe 1TG6 · UniProt Q16740
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