Research workbench
Staphylococcus aureus clpp mutant - Y63A
Analyse Staphylococcus aureus clpp mutant - Y63A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C90
- Type
- protein
- Length
- 2,558 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
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 12 distinct chains · 46% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 179 | 47% helix, 26% strand | Q2G036 |
| B | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 187 | 45% helix, 27% strand | Q2G036 |
| C | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 182 | 46% helix, 24% strand | Q2G036 |
| D | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 180 | 47% helix, 24% strand | Q2G036 |
| E | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 186 | 45% helix, 26% strand | Q2G036 |
| F, K | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 186 | 45% helix, 26% strand | Q2G036 |
| G | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 186 | 45% helix, 27% strand | Q2G036 |
| H, I | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 179 | 47% helix, 25% strand | Q2G036 |
| J | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 185 | 45% helix, 28% strand | Q2G036 |
| L | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 182 | 46% helix, 25% strand | Q2G036 |
| M | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 180 | 47% helix, 25% strand | Q2G036 |
| N | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 181 | 46% helix, 25% strand | Q2G036 |
Ligands and binding sites
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 14 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 | 707 | 0.73 | 0.79 | 96 | MPD |
| 2 | 733 | 0.73 | 0.78 | 105 | MPD |
| 3 | 580 | 0.72 | 0.80 | 77 | empty |
| 4 | 319 | 0.66 | 0.81 | 59 | empty |
| 5 | 333 | 0.65 | 0.80 | 47 | empty |
Interfaces
37 interfaces between chains.
- B–C · 1530 Ų buried · 10 hydrogen bonds · protein-protein
- F–G · 1496 Ų buried · 13 hydrogen bonds · protein-protein
- J–K · 1486 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1484 Ų buried · 12 hydrogen bonds · protein-protein
- K–L · 1381 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5C90 · Staphylococcus aureus ClpP mutant - Y63A · 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 5C90 · PDBe 5C90 · UniProt Q2G036
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