Research workbench
Clpx-clpp complex bound to ssra-tagged GFP, intermediate complex
Analyse Clpx-clpp complex bound to ssra-tagged GFP, intermediate complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WSG
- Type
- protein
- Length
- 3,334 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
- P0A6H1, P0A6G7, P42212
- Ligands
- AGS, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 9 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent clp protease ATP-binding subunit clpx | protein | 301 | 48% helix, 12% strand | P0A6H1 |
| B | ATP-dependent clp protease ATP-binding subunit clpx | protein | 334 | 45% helix, 13% strand | P0A6H1 |
| C | ATP-dependent clp protease ATP-binding subunit clpx | protein | 338 | 46% helix, 14% strand | P0A6H1 |
| D | ATP-dependent clp protease ATP-binding subunit clpx | protein | 338 | 45% helix, 14% strand | P0A6H1 |
| E | ATP-dependent clp protease ATP-binding subunit clpx | protein | 341 | 45% helix, 14% strand | P0A6H1 |
| F | ATP-dependent clp protease ATP-binding subunit clpx | protein | 331 | 45% helix, 13% strand | P0A6H1 |
| L, K, I, H | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 192 | 44% helix, 23% strand | P0A6G7 |
| J, N, M | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 191 | 45% helix, 23% strand | P0A6G7 |
| S | Green fluorescent protein, + ssra tag | protein | 10 | 0% helix, 30% strand | P42212 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 5 copies · chains B, C, D, E, F
- MG · Magnesium ion · metal · 4 copies · chains 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 983 | 0.84 | 0.85 | 89 | AGS |
| 2 | 689 | 0.83 | 0.87 | 77 | AGS, MG |
| 3 | 784 | 0.82 | 0.85 | 62 | AGS, MG |
| 4 | 762 | 0.82 | 0.85 | 61 | AGS, MG |
| 5 | 757 | 0.82 | 0.85 | 62 | AGS, MG |
Interfaces
34 interfaces between chains.
- D–E · 2301 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 2237 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 2221 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 2020 Ų buried · 16 hydrogen bonds · protein-protein
- L–M · 1789 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6WSG · ClpX-ClpP complex bound to ssrA-tagged GFP, intermediate complex · the same entry in another collection · chain I against I, 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 P0A6H1
- Every structure of UniProt P0A6G7
- Every structure of UniProt P42212
- Elsewhere: RCSB PDB 6WSG · PDBe 6WSG · UniProt P0A6H1 · UniProt P0A6G7 · UniProt P42212
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