Research workbench
Crystal structure of nucleotide-bound hexameric clpx
Analyse Crystal structure of nucleotide-bound hexameric clpx in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HWS
- Type
- protein
- Length
- 1,885 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent clp protease ATP-binding subunit clpx
- UniProt
- P0A6H1
- Ligands
- ADP, MG, SO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent clp protease ATP-binding subunit clpx | protein | 320 | 51% helix, 11% strand | P0A6H1 |
| B | ATP-dependent clp protease ATP-binding subunit clpx | protein | 315 | 54% helix, 12% strand | P0A6H1 |
| C | ATP-dependent clp protease ATP-binding subunit clpx | protein | 307 | 50% helix, 11% strand | P0A6H1 |
| D | ATP-dependent clp protease ATP-binding subunit clpx | protein | 316 | 52% helix, 11% strand | P0A6H1 |
| E | ATP-dependent clp protease ATP-binding subunit clpx | protein | 313 | 50% helix, 12% strand | P0A6H1 |
| F | ATP-dependent clp protease ATP-binding subunit clpx | protein | 314 | 50% helix, 13% strand | P0A6H1 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, D, E
- MG · Magnesium ion · metal · 2 copies · chains B, C, D
- SO4 · Sulfate ion · ion · 13 copies · chains A, B, C, D, 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 986 | 0.85 | 0.86 | 100 | ADP |
| 2 | 1188 | 0.84 | 0.85 | 104 | ADP |
| 3 | 991 | 0.83 | 0.84 | 93 | ADP, SO4, MG |
| 4 | 753 | 0.82 | 0.85 | 77 | ADP, SO4 |
| 5 | 942 | 0.81 | 0.83 | 106 | SO4, MG |
Interfaces
6 interfaces between chains.
- B–C · 1644 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1572 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1452 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 1448 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 1299 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3HWS · Crystal structure of nucleotide-bound hexameric ClpX · the same entry in another collection · chain B against B, TM-score 1.00
- P0A6H1 · AlphaFold monomer V2.0 prediction for ATP-dependent clp protease ATP- binding subunit… · a predicted model of the same protein · chain D against A, TM-score 0.95
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
- Elsewhere: RCSB PDB 3HWS · PDBe 3HWS · UniProt P0A6H1
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