Research workbench
The structure of streptococcus pneumoniae A153P clpp
Analyse The structure of streptococcus pneumoniae A153P clpp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Y7O
- Type
- protein
- Length
- 1,227 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
- P63788
- Ligands
- CA
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 7 distinct chains · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 171 | 46% helix, 22% strand | P63788 |
| B | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 178 | 44% helix, 23% strand | P63788 |
| C | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 176 | 43% helix, 20% strand | P63788 |
| D | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 178 | 43% helix, 23% strand | P63788 |
| E | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 174 | 45% helix, 22% strand | P63788 |
| F | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 173 | 45% helix, 20% strand | P63788 |
| G | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 177 | 44% helix, 23% strand | P63788 |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1102 | 0.74 | 0.77 | 113 | empty |
| 2 | 258 | 0.60 | 0.79 | 37 | empty |
| 3 | 325 | 0.60 | 0.77 | 38 | empty |
| 4 | 170 | 0.51 | 0.78 | 25 | empty |
| 5 | 200 | 0.48 | 0.75 | 36 | empty |
Interfaces
10 interfaces between chains.
- C–D · 1599 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1544 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1436 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 1406 Ų buried · 13 hydrogen bonds · protein-protein
- A–G · 1388 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 84 modified (engineered).
Compared structures
- 1Y7O · The structure of Streptococcus pneumoniae A153P ClpP · the same entry in another collection · chain G against G, TM-score 1.00
- P63788 · 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 0.98
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 P63788
- Elsewhere: RCSB PDB 1Y7O · PDBe 1Y7O · UniProt P63788
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