Research workbench
Clpx in clpx-clpp complex bound to substrate and ATP-gamma-S, class 4
Analyse Clpx in clpx-clpp complex bound to substrate and ATP-gamma-S, class 4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PP5
- Type
- protein
- Length
- 2,075 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent clp protease ATP-binding subunit clpx; Substrate peptide
- UniProt
- A0A1Q9L861
- Ligands
- AGS, ADP
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 6 distinct chains · 44% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent clp protease ATP-binding subunit clpx | protein | 341 | 43% helix, 13% strand | A0A1Q9L861 |
| B, C | ATP-dependent clp protease ATP-binding subunit clpx | protein | 352 | 44% helix, 13% strand | A0A1Q9L861 |
| D | ATP-dependent clp protease ATP-binding subunit clpx | protein | 347 | 44% helix, 12% strand | A0A1Q9L861 |
| E | ATP-dependent clp protease ATP-binding subunit clpx | protein | 348 | 42% helix, 9% strand | A0A1Q9L861 |
| F | ATP-dependent clp protease ATP-binding subunit clpx | protein | 323 | 49% helix, 9% strand | A0A1Q9L861 |
| S | Substrate peptide | protein | 12 | 0% helix, 17% strand | — |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 5 copies · chains A, B, C, D, E, F
- ADP · Adenosine-5'-diphosphate · ligand · chains 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 858 | 0.85 | 0.87 | 80 | AGS |
| 2 | 935 | 0.84 | 0.86 | 87 | ADP |
| 3 | 669 | 0.83 | 0.87 | 72 | AGS |
| 4 | 878 | 0.82 | 0.84 | 77 | AGS |
| 5 | 561 | 0.81 | 0.87 | 52 | AGS |
Interfaces
14 interfaces between chains.
- D–E · 2466 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 2340 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 2326 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2177 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 1768 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6PP5 · ClpX in ClpX-ClpP complex bound to substrate and ATP-gamma-S, class 4 · the same entry in another collection · chain B against B, 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 A0A1Q9L861
- Elsewhere: RCSB PDB 6PP5 · PDBe 6PP5 · UniProt A0A1Q9L861
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.