MolNFT v1 · #168796 · protein
Clpx-clpp complex bound to GFP-ssra, recognition complex
6WRF · ATP-dependent clp protease ATP-binding subunit clpx: “Clpx-clpp complex bound to GFP-ssra, recognition complex”. Electron microscopy, 3 ligands (AGS, ADP, MG), 20 pockets (best druggability 0.88). MolNFT v1 #168796 on GenesisL1: 3D…
- PDB
- 6WRF
- Type
- protein
- Length
- 3,450 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, ADP, MG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 9 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | ATP-dependent clp protease ATP-binding subunit clpx | protein | 352 | 43% helix, 13% strand | P0A6H1 |
| C, D | ATP-dependent clp protease ATP-binding subunit clpx | protein | 353 | 42% helix, 14% strand | P0A6H1 |
| E | ATP-dependent clp protease ATP-binding subunit clpx | protein | 347 | 43% helix, 13% strand | P0A6H1 |
| F | ATP-dependent clp protease ATP-binding subunit clpx | protein | 339 | 50% helix, 13% strand | P0A6H1 |
| H, I, J, K, L | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 192 | 44% helix, 21% strand | P0A6G7 |
| M | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 197 | 43% helix, 22% strand | P0A6G7 |
| N | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 191 | 45% helix, 21% strand | P0A6G7 |
| S | Green fluorescent protein | protein | 7 | 0% helix, 14% strand | P42212 |
| A | ATP-dependent clp protease ATP-binding subunit clpx | protein | 351 | 43% helix, 12% strand | P0A6H1 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 5 copies · chains B, C, D, E, F, A
- ADP · Adenosine-5'-diphosphate · ligand · chains F
- MG · Magnesium ion · metal · 5 copies · chains B, C, D, E, A
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 | 877 | 0.88 | 0.90 | 122 | empty |
| 2 | 844 | 0.82 | 0.85 | 71 | AGS, MG |
| 3 | 1108 | 0.82 | 0.83 | 90 | ADP |
| 4 | 751 | 0.82 | 0.85 | 63 | AGS, MG |
| 5 | 809 | 0.82 | 0.85 | 67 | AGS, MG |
Interfaces
39 interfaces between chains.
- B–C · 2497 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 2485 Ų buried · 25 hydrogen bonds · protein-protein
- D–E · 2416 Ų buried · 20 hydrogen bonds · protein-protein
- B–A · 2228 Ų buried · 27 hydrogen bonds · protein-protein
- E–F · 2101 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6WRF · ClpX-ClpP complex bound to GFP-ssrA, recognition complex · the same entry in another collection · chain M against M, 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 6WRF · PDBe 6WRF · UniProt P0A6H1 · UniProt P0A6G7 · UniProt P42212
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