MolNFT v1 · #63608 · protein
Crystal structure of the ATP-dependent clp protease clpc from clostridium difficile
3FES · ATP-dependent clp endopeptidase: “Crystal structure of the ATP-dependent clp protease clpc from clostridium difficile”. X-ray diffraction, 1 ligand (MG), 2 pockets (best druggability 0.83). MolNFT v1 #63608 on GenesisL1: 3D…
- PDB
- 3FES
- Type
- protein
- Length
- 565 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent clp endopeptidase
- UniProt
- Q18CA9
- Ligands
- MG
- Pockets
- 2 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 68% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | ATP-dependent clp endopeptidase | protein | 142 | 68% helix, 4% strand | Q18CA9 |
| B | ATP-dependent clp endopeptidase | protein | 141 | 67% helix, 4% strand | Q18CA9 |
| C | ATP-dependent clp endopeptidase | protein | 140 | 69% helix, 4% strand | Q18CA9 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- PG4 · Tetraethylene glycol · additive · 4 copies · chains A, B, C, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1089 | 0.83 | 0.85 | 97 | PG4, EPE |
| 2 | 137 | 0.60 | 0.85 | 24 | empty |
Interfaces
5 interfaces between chains.
- C–D · 637 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 457 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 452 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 221 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 125 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3FES · Crystal Structure of the ATP-dependent Clp Protease ClpC from Clostridium difficile · 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 Q18CA9
- Elsewhere: RCSB PDB 3FES · PDBe 3FES · UniProt Q18CA9
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