Research workbench
Structure of clpp from staphylococcus aureus in complex with acyldepsipeptide
Analyse Structure of clpp from staphylococcus aureus in complex with acyldepsipeptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PMD
- Type
- protein
- Length
- 2,614 residues
- Chains
- 25
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent clp protease proteolytic subunit; Shv-wfp-ser-pro-ycp-ala-MP8…
- EC
- 3.4.21.92
- UniProt
- Q2G036
- Ligands
- SHV
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 9 distinct chains · 46% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 184 | 46% helix, 26% strand | Q2G036 |
| B, C, L | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 182 | 46% helix, 26% strand | Q2G036 |
| D, S | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 182 | 46% helix, 26% strand | Q2G036 |
| E, N | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 182 | 46% helix, 25% strand | Q2G036 |
| F, G | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 181 | 46% helix, 25% strand | Q2G036 |
| I | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 183 | 46% helix, 26% strand | Q2G036 |
| K | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 183 | 46% helix, 26% strand | Q2G036 |
| M, T | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 181 | 46% helix, 25% strand | Q2G036 |
| H, J, O, P, Q, R, U, V, X, Y, Z | Shv-wfp-ser-pro-ycp-ala-MP8 acyldepsipeptide | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- SHV · Heptanoic acid · ligand · 11 copies · chains A, B, H, C, J, D, O, E, P, F, Q, G, R, K, L, U, M, V, N, X, S, T, Y, I, Z
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 14 copies · chains A, B, C, D, E, F, G, I, K, L, M, N, S, T
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 | 729 | 0.76 | 0.81 | 97 | empty |
| 2 | 712 | 0.69 | 0.76 | 93 | MPD |
| 3 | 475 | 0.68 | 0.79 | 70 | MPD |
| 4 | 300 | 0.66 | 0.82 | 43 | empty |
| 5 | 309 | 0.66 | 0.81 | 42 | empty |
Interfaces
57 interfaces between chains.
- N–S · 1430 Ų buried · 13 hydrogen bonds · protein-protein
- I–K · 1421 Ų buried · 11 hydrogen bonds · protein-protein
- M–N · 1394 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1378 Ų buried · 12 hydrogen bonds · protein-protein
- I–T · 1378 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 33 modified, 11 covalent (nonstandard, covalent ligand).
Compared structures
- 6PMD · Structure of ClpP from Staphylococcus aureus in complex with Acyldepsipeptide · the same entry in another collection · chain I against I, 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 6PMD · PDBe 6PMD · UniProt Q2G036
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