MolNFT v1 · #143837 · protein
Crystal structure of human mitochondrial clpp complex with acyldepsipeptide adep-28
6BBA · ATP-dependent clp protease proteolytic subunit…: “Crystal structure of human mitochondrial clpp complex with acyldepsipeptide adep-28”. X-ray diffraction, 2 ligands (SHV, 3A0), 19 pockets (best druggability 0.77). MolNFT v1 #143837…
- PDB
- 6BBA
- Type
- protein
- Length
- 1,353 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent clp protease proteolytic subunit, mitochondrial; Acyldepsipeptide adep-28
- EC
- 3.4.21.92
- UniProt
- Q16740
- Ligands
- SHV, 3A0
- Pockets
- 19 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | ATP-dependent clp protease proteolytic subunit, mitochondrial (EC 3.4.21.92) | protein | 189 | 40% helix, 22% strand | Q16740 |
| B | ATP-dependent clp protease proteolytic subunit, mitochondrial (EC 3.4.21.92) | protein | 185 | 42% helix, 22% strand | Q16740 |
| E, G | ATP-dependent clp protease proteolytic subunit, mitochondrial (EC 3.4.21.92) | protein | 188 | 41% helix, 21% strand | Q16740 |
| F | ATP-dependent clp protease proteolytic subunit, mitochondrial (EC 3.4.21.92) | protein | 190 | 41% helix, 22% strand | Q16740 |
| H, I, J, K, L, M, N | Acyldepsipeptide adep-28 | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- SHV · Heptanoic acid · ligand · 7 copies · chains A, G, H, B, I, C, J, D, K, E, L, F, M, N
- 3A0 · (2S,4S)-4-methylpiperidine-2-carboxylic acid · ligand · 7 copies · chains A, G, H, B, I, C, J, D, K, E, L, F, M, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 668 | 0.77 | 0.82 | 66 | empty |
| 2 | 445 | 0.76 | 0.84 | 58 | empty |
| 3 | 359 | 0.73 | 0.84 | 45 | empty |
| 4 | 71 | 0.52 | 0.86 | 13 | SHV |
| 5 | 65 | 0.50 | 0.85 | 14 | SHV |
Interfaces
21 interfaces between chains.
- F–G · 1682 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1654 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1642 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 1623 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1617 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 covalent, 14 modified (covalent ligand, nonstandard).
Compared structures
- 6BBA · Crystal structure of human mitochondrial ClpP complex with acyldepsipeptide ADEP-28 · the same entry in another collection · chain N against N, 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 6BBA · PDBe 6BBA · UniProt Q16740
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