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Crystal structure of clpp from staphylococcus aureus
Analyse Crystal structure of clpp from staphylococcus aureus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QWD
- Type
- protein
- Length
- 2,589 residues
- Chains
- 14
- 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
- Q2G036
- Ligands
- CL
- Pockets
- 20 · best druggability 0.65
Structure
x-ray diffraction · 13 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 187 | 43% helix, 21% strand | Q2G036 |
| B | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 187 | 43% helix, 21% strand | Q2G036 |
| C | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 186 | 44% helix, 20% strand | Q2G036 |
| D | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 182 | 45% helix, 21% strand | Q2G036 |
| E | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 188 | 43% helix, 21% strand | Q2G036 |
| F | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 182 | 45% helix, 19% strand | Q2G036 |
| G | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 185 | 44% helix, 20% strand | Q2G036 |
| H | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 192 | 42% helix, 20% strand | Q2G036 |
| I | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 186 | 44% helix, 20% strand | Q2G036 |
| J, M | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 186 | 44% helix, 20% strand | Q2G036 |
| K | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 179 | 45% helix, 20% strand | Q2G036 |
| L | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 180 | 45% helix, 19% strand | Q2G036 |
| N | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 183 | 44% helix, 21% strand | Q2G036 |
Ligands and binding sites
- CL · Chloride ion · ion · 7 copies · chains A, B, C, D, L, M
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 | 193 | 0.65 | 0.84 | 41 | empty |
| 2 | 296 | 0.62 | 0.79 | 48 | empty |
| 3 | 214 | 0.61 | 0.81 | 36 | empty |
| 4 | 226 | 0.60 | 0.80 | 37 | empty |
| 5 | 111 | 0.59 | 0.86 | 23 | empty |
Interfaces
14 interfaces between chains.
- H–N · 1738 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 1662 Ų buried · 19 hydrogen bonds · protein-protein
- A–G · 1662 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1646 Ų buried · 10 hydrogen bonds · protein-protein
- L–M · 1627 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3QWD · Crystal structure of ClpP from Staphylococcus aureus · the same entry in another collection · chain K against K, 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 Q2G036
- Elsewhere: RCSB PDB 3QWD · PDBe 3QWD · UniProt Q2G036
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