Research workbench
Structure of clpp from staphylococcus aureus in complex with ureadepsipeptide
Analyse Structure of clpp from staphylococcus aureus in complex with ureadepsipeptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PKA
- Type
- protein
- Length
- 2,594 residues
- Chains
- 28
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent clp protease proteolytic subunit; OO1-wfp-ser-pro-ycp-ala-MP8…
- EC
- 3.4.21.92
- UniProt
- Q2G036
- Ligands
- OO1
- Pockets
- 20 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E, F, G, I, K, L, S, T | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 179 | 47% helix, 25% strand | Q2G036 |
| B, C, M, N | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 180 | 47% helix, 25% strand | Q2G036 |
| H, J, O, P, Q, R, U, V, X, Y, Z, a, b, c | OO1-wfp-ser-pro-ycp-ala-MP8 ureadepsipeptide | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- OO1 · (4-methylphenyl)carbamic acid · ligand · 14 copies · chains A, B, H, C, J, D, O, E, P, F, Q, G, R, U, I, K, V, L, X, M, Y, N, Z, S, a, T, b, c
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 | 454 | 0.66 | 0.78 | 62 | empty |
| 2 | 465 | 0.66 | 0.78 | 60 | empty |
| 3 | 399 | 0.65 | 0.79 | 59 | empty |
| 4 | 425 | 0.65 | 0.78 | 66 | empty |
| 5 | 390 | 0.64 | 0.78 | 58 | empty |
Interfaces
63 interfaces between chains.
- M–N · 1262 Ų buried · 12 hydrogen bonds · protein-protein
- K–L · 1253 Ų buried · 10 hydrogen bonds · protein-protein
- F–G · 1247 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1245 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 1233 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 modified, 14 covalent (nonstandard, covalent ligand).
Compared structures
- 6PKA · Structure of ClpP from Staphylococcus aureus in complex with ureadepsipeptide · 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 Q2G036
- Elsewhere: RCSB PDB 6PKA · PDBe 6PKA · UniProt Q2G036
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