MolNFT v1 · #145769 · protein
Crystal structure of clostridium perfringens beta-glucuronidase bound with a novel, potent inhibitor 4-(8-(piperazin-1-yl)-1,2,3,4- tetrahydro-[1,2,3]TRIAZINO[4',5':4,5]THIENO[2,3-C]ISOQUINOLIN-5-yl) morpholine
6CXS: “Crystal structure of clostridium perfringens beta-glucuronidase bound with a novel, potent inhibitor…”. X-ray diffraction, 1 ligand (FJV), 17 pockets (best druggability 0.85). MolNFT v1 #145769 on GenesisL1: 3D structure, binding…
- PDB
- 6CXS
- Type
- protein
- Length
- 1,811 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucuronidase; MALTOSE/MALTODEXTRIN-binding periplasmic protein
- UniProt
- Q8XP19, P0AEX9
- Ligands
- FJV
- Pockets
- 17 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-glucuronidase | protein | 598 | 19% helix, 36% strand | Q8XP19 |
| B | Beta-glucuronidase | protein | 599 | 19% helix, 35% strand | Q8XP19 |
| C | MALTOSE/MALTODEXTRIN-binding periplasmic protein | protein | 252 | 37% helix, 15% strand | P0AEX9 |
| D | MALTOSE/MALTODEXTRIN-binding periplasmic protein | protein | 362 | 41% helix, 19% strand | P0AEX9 |
Ligands and binding sites
- FJV · 4-(8-(piperazin-1-yl)-1,2,3,4-tetrahydro-[1,2, 3]triazino[4',5':4,5]thieno[2,3-c]isoquinolin-5-yl) morpholine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1096 | 0.85 | 0.86 | 128 | empty |
| 2 | 288 | 0.80 | 0.92 | 33 | empty |
| 3 | 313 | 0.79 | 0.90 | 34 | empty |
| 4 | 293 | 0.77 | 0.89 | 37 | empty |
| 5 | 598 | 0.71 | 0.79 | 73 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2072 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 801 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 753 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6CXS · Crystal Structure of Clostridium perfringens beta-glucuronidase bound with a novel… · 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 6CXS · PDBe 6CXS · UniProt Q8XP19 · UniProt P0AEX9
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