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Crystal structure of clostridium difficile toxin B (tcdb) glucosyltransferase in complex with udp and isofagomine
Analyse Crystal structure of clostridium difficile toxin B (tcdb) glucosyltransferase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LOU
- Type
- protein
- Length
- 1,085 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucosyltransferase tcdb
- EC
- 2.4.1.-
- UniProt
- P18177
- Ligands
- UDP, IFM, MN
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucosyltransferase tcdb (EC 2.4.1.-) | protein | 545 | 57% helix, 8% strand | P18177 |
| B | Glucosyltransferase tcdb (EC 2.4.1.-) | protein | 540 | 59% helix, 8% strand | P18177 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- IFM · 5-hydroxymethyl-3,4-dihydroxypiperidine · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 19 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 955 | 0.82 | 0.83 | 77 | UDP, IFM, MN |
| 2 | 707 | 0.79 | 0.83 | 67 | UDP, IFM, MN |
| 3 | 182 | 0.64 | 0.85 | 28 | empty |
| 4 | 174 | 0.48 | 0.76 | 28 | empty |
| 5 | 68 | 0.44 | 0.82 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1654 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 7LOU · Crystal structure of Clostridium difficile Toxin B (TcdB) glucosyltransferase in complex… · 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 7LOU · PDBe 7LOU · UniProt P18177
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