MolNFT v1 · #37389 · protein
Crystal structure of E. COLI clpp with a peptide chloromethyl ketone covalently bound at the active site
2FZS · ATP-dependent clp protease proteolytic subunit: “Crystal structure of E. COLI clpp with a peptide chloromethyl ketone covalently bound at the active site”. X-ray diffraction, 1 ligand (CMQ), 20 pockets (best druggability 0.80).…
- PDB
- 2FZS
- Type
- protein
- Length
- 2,591 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
- CMQ
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 8 distinct chains · 45% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, K | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 186 | 45% helix, 27% strand | P0A6G7 |
| B | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 192 | 44% helix, 27% strand | P0A6G7 |
| C | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 183 | 45% helix, 24% strand | P0A6G7 |
| D, J | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 185 | 45% helix, 25% strand | P0A6G7 |
| E | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 188 | 44% helix, 28% strand | P0A6G7 |
| F | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 185 | 45% helix, 26% strand | P0A6G7 |
| G, H, I, L, N | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 183 | 46% helix, 24% strand | P0A6G7 |
| M | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 186 | 45% helix, 26% strand | P0A6G7 |
Ligands and binding sites
- CMQ · N~2~-[(benzyloxy)carbonyl]-N-[(1S,2S)-2-hydroxy-1-(4-hydroxybenzyl)propyl]-L-leucinamide · ligand · 14 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N
- PGE · Triethylene glycol · additive · 15 copies · chains A, G, B, C, D, E, F, H, I, J, K, L, M, N
- GOL · Glycerol · additive · 11 copies · chains A, G, B, C, D, E, F, H, I, K, L, M, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 979 | 0.80 | 0.81 | 127 | empty |
| 2 | 932 | 0.78 | 0.80 | 121 | CMQ, GOL |
| 3 | 809 | 0.77 | 0.81 | 100 | CMQ, GOL |
| 4 | 752 | 0.77 | 0.81 | 101 | GOL, CMQ |
| 5 | 621 | 0.77 | 0.83 | 81 | CMQ, GOL |
Interfaces
38 interfaces between chains.
- A–G · 1813 Ų buried · 23 hydrogen bonds · protein-protein
- K–L · 1780 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1724 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1710 Ų buried · 25 hydrogen bonds · protein-protein
- J–K · 1710 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 25 covalent (covalent ligand).
Compared structures
- 2FZS · Crystal structure of E. coli ClpP with a Peptide Chloromethyl Ketone Covalently Bound at… · the same entry in another collection · chain K against K, 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 2FZS · PDBe 2FZS · UniProt P0A6G7
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