Research workbench
Crystal structure of pseudomonas aeruginosa CLPP1
Analyse Crystal structure of pseudomonas aeruginosa CLPP1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7M1M
- Type
- protein
- Length
- 2,554 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
- A0A072ZHR6
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, F, G, H, I, L, M, N | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 182 | 46% helix, 25% strand | A0A072ZHR6 |
| C, J | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 183 | 46% helix, 26% strand | A0A072ZHR6 |
| D, K | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 183 | 46% helix, 25% strand | A0A072ZHR6 |
| E | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 184 | 46% helix, 26% strand | A0A072ZHR6 |
Ligands and binding sites
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 18 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 787 | 0.75 | 0.79 | 100 | MPD |
| 2 | 701 | 0.75 | 0.80 | 81 | MPD |
| 3 | 852 | 0.73 | 0.77 | 106 | empty |
| 4 | 627 | 0.73 | 0.79 | 67 | MPD |
| 5 | 553 | 0.71 | 0.79 | 67 | empty |
Interfaces
35 interfaces between chains.
- D–E · 1683 Ų buried · 21 hydrogen bonds · protein-protein
- J–K · 1681 Ų buried · 20 hydrogen bonds · protein-protein
- F–G · 1646 Ų buried · 20 hydrogen bonds · protein-protein
- H–N · 1643 Ų buried · 18 hydrogen bonds · protein-protein
- H–I · 1638 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 7M1M · Crystal structure of Pseudomonas aeruginosa ClpP1 · the same entry in another collection · chain A against A, 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 A0A072ZHR6
- Elsewhere: RCSB PDB 7M1M · PDBe 7M1M · UniProt A0A072ZHR6
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