Research workbench
Clpx-clpp complex bound to substrate and ATP-gamma-S, class 3
Analyse Clpx-clpp complex bound to substrate and ATP-gamma-S, class 3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PO3
- Type
- protein
- Length
- 3,412 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent clp protease ATP-binding subunit clpx; ATP-dependent clp protease…
- EC
- 3.4.21.92
- UniProt
- A0A1Q9L861, S1IIE7
- Ligands
- AGS, ADP
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 8 distinct chains · 44% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent clp protease ATP-binding subunit clpx | protein | 344 | 46% helix, 12% strand | A0A1Q9L861 |
| B | ATP-dependent clp protease ATP-binding subunit clpx | protein | 346 | 45% helix, 11% strand | A0A1Q9L861 |
| C | ATP-dependent clp protease ATP-binding subunit clpx | protein | 346 | 44% helix, 10% strand | A0A1Q9L861 |
| D | ATP-dependent clp protease ATP-binding subunit clpx | protein | 349 | 44% helix, 11% strand | A0A1Q9L861 |
| E | ATP-dependent clp protease ATP-binding subunit clpx | protein | 345 | 44% helix, 11% strand | A0A1Q9L861 |
| F | ATP-dependent clp protease ATP-binding subunit clpx | protein | 331 | 44% helix, 11% strand | A0A1Q9L861 |
| H, I, J, K, L, M, N | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 192 | 44% helix, 23% strand | S1IIE7 |
| S | Substrate peptide | protein | 7 | 0% helix, 0% 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 | 1044 | 0.84 | 0.85 | 98 | ADP |
| 2 | 962 | 0.84 | 0.85 | 98 | AGS |
| 3 | 919 | 0.84 | 0.86 | 104 | empty |
| 4 | 933 | 0.84 | 0.85 | 74 | AGS |
| 5 | 670 | 0.83 | 0.87 | 79 | AGS |
Interfaces
36 interfaces between chains.
- D–E · 2341 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 2260 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 2257 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 2080 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 1909 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6PO3 · ClpX-ClpP complex bound to substrate and ATP-gamma-S, class 3 · the same entry in another collection · chain A against A, 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
- Every structure of UniProt S1IIE7
- Elsewhere: RCSB PDB 6PO3 · PDBe 6PO3 · UniProt A0A1Q9L861 · UniProt S1IIE7
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