Research workbench
Clostridial cysteine protease CWP84 C116A after propeptide cleavage
Analyse Clostridial cysteine protease CWP84 C116A after propeptide cleavage in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4D59
- Type
- protein
- Length
- 812 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell surface protein (putative cell surface-associated cysteine protease)
- EC
- 3.4.22.15
- UniProt
- C9YQ11
- Ligands
- JEF, CA
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cell surface protein (putative cell surface-associated cysteine protease) (EC 3.4.22.15) | protein | 406 | 15% helix, 35% strand | C9YQ11 |
Ligands and binding sites
- JEF · O-(O-(2-aminopropyl)-O'-(2-methoxyethyl)polypropylene glycol 500) · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 761 | 0.66 | 0.74 | 80 | empty |
| 2 | 102 | 0.46 | 0.79 | 23 | empty |
| 3 | 136 | 0.41 | 0.74 | 22 | empty |
| 4 | 81 | 0.36 | 0.77 | 16 | empty |
| 5 | 108 | 0.36 | 0.73 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 237 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4D59 · Clostridial Cysteine protease Cwp84 C116A after propeptide cleavage · 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 C9YQ11
- Elsewhere: RCSB PDB 4D59 · PDBe 4D59 · UniProt C9YQ11
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