MolNFT v1 · #137779 · protein
Structure of clpp from staphylococcus aureus in complex with acyldepsipeptide
5VZ2 · ATP-dependent clp protease proteolytic subunit: “Structure of clpp from staphylococcus aureus in complex with acyldepsipeptide”. X-ray diffraction, 1 ligand (9TS), 20 pockets (best druggability 0.73). MolNFT v1 #137779 on GenesisL1…
- PDB
- 5VZ2
- Type
- protein
- Length
- 2,587 residues
- Chains
- 28
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent clp protease proteolytic subunit; Acyldepsipeptide
- EC
- 3.4.21.92
- UniProt
- Q2G036
- Ligands
- 9TS
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 9 distinct chains · 47% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F, I, L, M, S | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 179 | 47% helix, 24% strand | Q2G036 |
| B | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 179 | 47% helix, 24% strand | Q2G036 |
| C | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 178 | 47% helix, 24% strand | Q2G036 |
| D | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 177 | 47% helix, 24% strand | Q2G036 |
| E | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 178 | 47% helix, 24% strand | Q2G036 |
| G | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 180 | 47% helix, 25% strand | Q2G036 |
| K, N | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 178 | 47% helix, 24% strand | Q2G036 |
| T | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 181 | 46% helix, 24% strand | Q2G036 |
| H, J, O, P, Q, R, U, V, X, Y, Z, a, b, c | Acyldepsipeptide | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- 9TS · (2E)-pent-2-enoic 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 754 | 0.73 | 0.78 | 107 | empty |
| 2 | 438 | 0.65 | 0.78 | 64 | empty |
| 3 | 297 | 0.63 | 0.80 | 50 | empty |
| 4 | 317 | 0.62 | 0.79 | 49 | empty |
| 5 | 376 | 0.62 | 0.78 | 51 | empty |
Interfaces
63 interfaces between chains.
- A–G · 1332 Ų buried · 11 hydrogen bonds · protein-protein
- M–N · 1300 Ų buried · 14 hydrogen bonds · protein-protein
- I–T · 1297 Ų buried · 13 hydrogen bonds · protein-protein
- I–K · 1296 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 1290 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified, 14 covalent (nonstandard, covalent ligand).
Compared structures
- 5VZ2 · Structure of ClpP from Staphylococcus aureus in complex with Acyldepsipeptide · the same entry in another collection · chain M against M, 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 5VZ2 · PDBe 5VZ2 · UniProt Q2G036
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.