Research workbench
Crystal structure of the clostridium perfringens spore cortex lytic enzyme slem
Analyse Crystal structure of the clostridium perfringens spore cortex lytic enzyme slem in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JIP
- Type
- protein
- Length
- 631 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cortical-lytic enzyme
- UniProt
- O06496
- Ligands
- MG
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cortical-lytic enzyme | protein | 317 | 22% helix, 30% strand | O06496 |
| B | Cortical-lytic enzyme | protein | 314 | 23% helix, 29% strand | O06496 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1122 | 0.81 | 0.83 | 127 | empty |
| 2 | 242 | 0.48 | 0.74 | 35 | empty |
| 3 | 158 | 0.46 | 0.76 | 23 | empty |
| 4 | 217 | 0.45 | 0.73 | 32 | empty |
| 5 | 73 | 0.38 | 0.78 | 20 | MES |
Interfaces
1 interface between chains.
- A–B · 1184 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 5JIP · Crystal structure of the Clostridium perfringens spore cortex lytic enzyme SleM · 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 O06496
- Elsewhere: RCSB PDB 5JIP · PDBe 5JIP · UniProt O06496
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