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Structure of thermus thermophilus clpp in complex with a tripeptide.
Analyse Structure of thermus thermophilus clpp in complex with a tripeptide. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HWN
- Type
- protein
- Length
- 1,326 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent clp protease proteolytic subunit; Unknown tripeptide
- EC
- 3.4.21.92
- UniProt
- Q72L15
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 7 distinct chains · 45% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 187 | 46% helix, 22% strand | Q72L15 |
| H, I, J, K, L, M, N | Unknown tripeptide | protein | 3 | 0% helix, 33% strand | — |
| B | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 186 | 45% helix, 24% strand | Q72L15 |
| C | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 188 | 45% helix, 23% strand | Q72L15 |
| E | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 186 | 45% helix, 24% strand | Q72L15 |
| F | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 187 | 45% helix, 22% strand | Q72L15 |
| G | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 184 | 46% helix, 22% strand | Q72L15 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 17 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 581 | 0.77 | 0.83 | 84 | empty |
| 2 | 138 | 0.63 | 0.86 | 22 | empty |
| 3 | 279 | 0.60 | 0.79 | 40 | empty |
| 4 | 274 | 0.59 | 0.79 | 33 | empty |
| 5 | 266 | 0.59 | 0.79 | 33 | empty |
Interfaces
15 interfaces between chains.
- F–G · 1574 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1573 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1544 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 1540 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1533 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6HWN · Structure of Thermus thermophilus ClpP in complex with a tripeptide. · 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 Q72L15
- Elsewhere: RCSB PDB 6HWN · PDBe 6HWN · UniProt Q72L15
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