MolNFT v1 · #165398 · protein
Structure of the CLPP:ADEP4-complex from staphylococcus aureus (open state)
6TTZ · ATP-dependent clp protease proteolytic subunit: “Structure of the CLPP:ADEP4-complex from staphylococcus aureus (open state)”. X-ray diffraction, 1 ligand (NWT), 20 pockets (best druggability 0.81). MolNFT v1 #165398 on GenesisL1…
- PDB
- 6TTZ
- Type
- protein
- Length
- 1,322 residues
- Chains
- 7
- 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
- A0A077UUA2
- Ligands
- NWT
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 45% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 190 | 45% helix, 24% strand | A0A077UUA2 |
| B | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 186 | 45% helix, 23% strand | A0A077UUA2 |
| C | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 186 | 45% helix, 23% strand | A0A077UUA2 |
| D | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 189 | 44% helix, 24% strand | A0A077UUA2 |
| E, F | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 191 | 44% helix, 23% strand | A0A077UUA2 |
| G | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 189 | 44% helix, 24% strand | A0A077UUA2 |
Ligands and binding sites
- NWT · N-[(2S)-3-(3,5-difluorophenyl)-1-[[(3S,9S,13S,15R,19S, 22S)-15,19-dimethyl-2,8,12,18,21-pentaoxo-11-oxa-1,7, 17,20-tetrazatetracyclo[20.4.0.03,7.013,17]hexacosan-9-yl]amino]-1-oxopropan-2-yl]heptanamide · ligand · 7 copies · chains A, G, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1150 | 0.81 | 0.82 | 145 | empty |
| 2 | 287 | 0.56 | 0.77 | 53 | empty |
| 3 | 272 | 0.56 | 0.77 | 51 | empty |
| 4 | 212 | 0.54 | 0.77 | 44 | empty |
| 5 | 163 | 0.52 | 0.78 | 23 | NWT |
Interfaces
8 interfaces between chains.
- F–G · 1604 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1576 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 1575 Ų buried · 16 hydrogen bonds · protein-protein
- A–G · 1515 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1508 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6TTZ · Structure of the ClpP:ADEP4-complex from Staphylococcus aureus (open state) · 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 A0A077UUA2
- Elsewhere: RCSB PDB 6TTZ · PDBe 6TTZ · UniProt A0A077UUA2
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