MolNFT v1 · #157801 · protein
Crystal structure of escherichia COLI clpp protease complexed with small molecule activator, ACP1-06
6NB1 · ATP-dependent clp protease proteolytic subunit: “Crystal structure of escherichia COLI clpp protease complexed with small molecule activator, ACP1-06”. X-ray diffraction, 1 ligand (KHS), 20 pockets (best druggability 0.78). MolNFT…
- PDB
- 6NB1
- Type
- protein
- Length
- 2,561 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
- P0A6G7
- Ligands
- KHS
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 13 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 | 188 | 45% helix, 27% strand | P0A6G7 |
| B | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 193 | 43% helix, 27% strand | P0A6G7 |
| C | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 184 | 45% helix, 25% strand | P0A6G7 |
| D | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 184 | 46% helix, 25% strand | P0A6G7 |
| E | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 186 | 45% helix, 26% strand | P0A6G7 |
| F | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 183 | 45% helix, 25% strand | P0A6G7 |
| G | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 183 | 46% helix, 24% strand | P0A6G7 |
| H | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 181 | 46% helix, 25% strand | P0A6G7 |
| I | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 176 | 47% helix, 25% strand | P0A6G7 |
| J | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 180 | 47% helix, 24% strand | P0A6G7 |
| K | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 181 | 46% helix, 24% strand | P0A6G7 |
| L | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 182 | 46% helix, 25% strand | P0A6G7 |
| M, N | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 180 | 46% helix, 24% strand | P0A6G7 |
Ligands and binding sites
- KHS · N-{2-[(2-chlorophenyl)sulfanyl]ethyl}-2-methyl-2-{[5-(trifluoromethyl)pyridin-2-yl]sulfonyl}propanamide · ligand · 14 copies · chains A, G, B, C, D, E, F, H, I, J, K, L, M, N
- GOL · Glycerol · additive · 14 copies · chains A, B, C, D, E, F, G, H, N, I, J, K, L, M
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 | 1056 | 0.78 | 0.80 | 130 | GOL |
| 2 | 945 | 0.78 | 0.80 | 124 | GOL |
| 3 | 848 | 0.77 | 0.80 | 114 | GOL |
| 4 | 734 | 0.76 | 0.81 | 92 | GOL |
| 5 | 723 | 0.76 | 0.81 | 83 | GOL |
Interfaces
37 interfaces between chains.
- C–D · 1739 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1714 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 1697 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 1695 Ų buried · 23 hydrogen bonds · protein-protein
- A–G · 1686 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6NB1 · Crystal structure of Escherichia coli ClpP protease complexed with small molecule… · the same entry in another collection · chain F against F, 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 P0A6G7
- Elsewhere: RCSB PDB 6NB1 · PDBe 6NB1 · UniProt P0A6G7
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