MolNFT v1 · #181239 · protein
Crystal structure of clostridium difficile toxin B (tcdb) glucosyltransferase in complex with udp and noeuromycin
7LOV: “Crystal structure of clostridium difficile toxin B (tcdb) glucosyltransferase in complex with udp and…”. X-ray diffraction, 3 ligands (NOY, UDP, MN), 8 pockets (best druggability 0.77). MolNFT v1 #181239 on GenesisL1: 3D structure…
- PDB
- 7LOV
- Type
- protein
- Length
- 1,077 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
- NOY, UDP, MN
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toxin B (EC 3.4.22.-) | protein | 539 | 58% helix, 8% strand | P18177 |
| B | Toxin B (EC 3.4.22.-) | protein | 538 | 59% helix, 8% strand | P18177 |
Ligands and binding sites
- NOY · (2R,3S,4R,5R)-5-(hydroxymethyl)piperidine-2,3,4-triol · ligand · 2 copies · chains A, B
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1136 | 0.77 | 0.79 | 109 | NOY, UDP, GOL, MN |
| 2 | 831 | 0.77 | 0.80 | 85 | NOY, UDP, MN |
| 3 | 229 | 0.56 | 0.78 | 36 | empty |
| 4 | 163 | 0.48 | 0.77 | 27 | empty |
| 5 | 114 | 0.41 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 630 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7LOV · 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 7LOV · PDBe 7LOV · UniProt P18177
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