MolNFT v1 · #79096 · protein
Crystal structure of clpp in heptameric form from staphylococcus aureus
3ST9 · ATP-dependent clp protease proteolytic subunit: “Crystal structure of clpp in heptameric form from staphylococcus aureus”. X-ray diffraction, 2 ligands (CA, SO4), 17 pockets (best druggability 0.51). MolNFT v1 #79096 on GenesisL1…
- PDB
- 3ST9
- Type
- protein
- Length
- 1,200 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent clp protease proteolytic subunit
- EC
- 3.4.21.92
- UniProt
- P63786
- Ligands
- CA, SO4
- Pockets
- 17 · best druggability 0.51
Structure
x-ray diffraction · 5 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 170 | 48% helix, 19% strand | P63786 |
| C, D | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 171 | 48% helix, 19% strand | P63786 |
| E | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 172 | 47% helix, 19% strand | P63786 |
| F | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 173 | 46% helix, 20% strand | P63786 |
| G | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 173 | 47% helix, 19% strand | P63786 |
Ligands and binding sites
- CA · Calcium ion · metal · chains B
- SO4 · Sulfate ion · ion · 2 copies · chains A, D
- GOL · Glycerol · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 120 | 0.51 | 0.81 | 20 | empty |
| 2 | 138 | 0.50 | 0.79 | 22 | empty |
| 3 | 96 | 0.50 | 0.82 | 23 | empty |
| 4 | 133 | 0.47 | 0.78 | 20 | empty |
| 5 | 168 | 0.47 | 0.76 | 24 | empty |
Interfaces
7 interfaces between chains.
- B–G · 1320 Ų buried · 9 hydrogen bonds · protein-protein
- A–F · 1320 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 1250 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 1249 Ų buried · 6 hydrogen bonds · protein-protein
- A–G · 1244 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3ST9 · Crystal structure of ClpP in heptameric form from Staphylococcus aureus · the same entry in another collection · chain G against G, TM-score 1.00
- P63786 · AlphaFold monomer V2.0 prediction for ATP-dependent clp protease proteolytic subunit… · a predicted model of the same protein · chain A against A, TM-score 0.92
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 P63786
- Elsewhere: RCSB PDB 3ST9 · PDBe 3ST9 · UniProt P63786
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