Research workbench
Clpp from staphylococcus aureus in complex with AV145
Analyse Clpp from staphylococcus aureus in complex with AV145 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DL1
- Type
- protein
- Length
- 2,632 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
- Q2YSF8
- Ligands
- 5C2
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 188 | 43% helix, 19% strand | Q2YSF8 |
Ligands and binding sites
- 5C2 · 1-(propan-2-yl)-N-{[2-(thiophen-2-yl)-1,3-oxazol-4-yl]methyl}-1H-pyrazolo[3,4-b]pyridine-5-carboxamide · ligand · 14 copies · chains A, N, B, K, C, J, D, I, E, M, F, L, G, H
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 | 796 | 0.83 | 0.86 | 104 | 5C2 |
| 2 | 739 | 0.82 | 0.85 | 96 | 5C2 |
| 3 | 814 | 0.81 | 0.84 | 106 | 5C2 |
| 4 | 834 | 0.81 | 0.84 | 102 | 5C2 |
| 5 | 788 | 0.80 | 0.83 | 92 | 5C2 |
Interfaces
35 interfaces between chains.
- M–N · 1765 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1760 Ų buried · 21 hydrogen bonds · protein-protein
- L–M · 1757 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1747 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 1746 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 5DL1 · ClpP from Staphylococcus aureus in complex with AV145 · 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 Q2YSF8
- Elsewhere: RCSB PDB 5DL1 · PDBe 5DL1 · UniProt Q2YSF8
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