Research workbench
Crystal structure of clostridium perfringens beta-glucuronidase
Analyse Crystal structure of clostridium perfringens beta-glucuronidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JKM
- Type
- protein
- Length
- 1,818 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucuronidase; Maltose-binding periplasmic protein
- EC
- 3.2.1.31
- UniProt
- Q8XP19, P0AEX9
- Pockets
- 18 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-glucuronidase (EC 3.2.1.31) | protein | 602 | 19% helix, 35% strand | Q8XP19 |
| D | Maltose-binding periplasmic protein | protein | 362 | 42% helix, 19% strand | P0AEX9 |
| C | Maltose-binding periplasmic protein | protein | 252 | 37% helix, 17% strand | P0AEX9 |
Pockets
18 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 917 | 0.88 | 0.90 | 82 | empty |
| 2 | 688 | 0.84 | 0.88 | 77 | empty |
| 3 | 1191 | 0.78 | 0.80 | 116 | empty |
| 4 | 643 | 0.73 | 0.80 | 84 | empty |
| 5 | 251 | 0.67 | 0.83 | 42 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2125 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 822 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 757 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4JKM · Crystal Structure of Clostridium perfringens beta-glucuronidase · 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 Q8XP19
- Every structure of UniProt P0AEX9
- Elsewhere: RCSB PDB 4JKM · PDBe 4JKM · UniProt Q8XP19 · UniProt P0AEX9
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