Research workbench
Structure of the clostridium perfringens cspb protease
Analyse Structure of the clostridium perfringens cspb protease in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4I0W
- Type
- protein
- Length
- 1,122 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease cspb
- EC
- 3.4.-.-
- UniProt
- Q0TM89
- Ligands
- NA, CL
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Protease cspb (EC 3.4.-.-) | protein | 92 | 37% helix, 32% strand | Q0TM89 |
| B | Protease cspb (EC 3.4.-.-) | protein | 464 | 24% helix, 30% strand | Q0TM89 |
| D | Protease cspb (EC 3.4.-.-) | protein | 474 | 24% helix, 29% strand | Q0TM89 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains B, D
- CL · Chloride ion · ion · 3 copies · chains B, D
- EDO · 1,2-ethanediol · additive · 8 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 487 | 0.83 | 0.90 | 72 | EDO |
| 2 | 187 | 0.76 | 0.91 | 35 | EDO |
| 3 | 792 | 0.75 | 0.79 | 66 | empty |
| 4 | 595 | 0.71 | 0.79 | 62 | empty |
| 5 | 278 | 0.68 | 0.83 | 38 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1671 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1564 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 1534 Ų buried · 33 hydrogen bonds · protein-protein
- A–D · 372 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 365 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified, 2 disulfide (engineered, disulfide).
Compared structures
- 4I0W · Structure of the Clostridium Perfringens CspB protease · 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 Q0TM89
- Elsewhere: RCSB PDB 4I0W · PDBe 4I0W · UniProt Q0TM89
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