MolNFT v1 · #136370 · protein
Clostridium difficile toxin B (tcdb) glucosyltransferase domain co- crystallized with apigenin
5UQT: “Clostridium difficile toxin B (tcdb) glucosyltransferase domain co- crystallized with apigenin”. X-ray diffraction, 2 ligands (AGI, MN), 9 pockets (best druggability 0.73). MolNFT v1 #136370 on GenesisL1: 3D structure, binding sites…
- PDB
- 5UQT
- Type
- protein
- Length
- 1,076 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toxin B
- EC
- 3.4.22.-
- UniProt
- P18177
- Ligands
- AGI, MN
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 60% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Toxin B (EC 3.4.22.-) | protein | 538 | 60% helix, 8% strand | P18177 |
Ligands and binding sites
- AGI · 5,7-dihydroxy-2-(4-hydroxyphenyl)-4H-chromen-4-one · ligand · chains A, B
- MN · Manganese (II) ion · metal · 2 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1000 | 0.73 | 0.76 | 61 | MN |
| 2 | 1184 | 0.72 | 0.76 | 107 | MN, AGI |
| 3 | 239 | 0.56 | 0.78 | 34 | empty |
| 4 | 268 | 0.54 | 0.76 | 35 | empty |
| 5 | 151 | 0.47 | 0.77 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 692 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5UQT · Clostridium difficile Toxin B (TcdB) glucosyltransferase domain co-crystallized with… · 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 P18177
- Elsewhere: RCSB PDB 5UQT · PDBe 5UQT · UniProt P18177
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