MolNFT v1 · #117154 · protein
C3LARVIN toxin, an ADP-ribosyltransferase from paenibacillus larvae, orthorhombic form
5DZQ · Toxin-like protein: “C3LARVIN toxin, an ADP-ribosyltransferase from paenibacillus larvae, orthorhombic form”. X-ray diffraction, 1 ligand (MG), 5 pockets (best druggability 0.81). MolNFT v1 #117154 on GenesisL1: 3D structure…
- PDB
- 5DZQ
- Type
- protein
- Length
- 360 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toxin-like protein
- EC
- 2.4.2.30
- UniProt
- W2E3J5
- Ligands
- MG
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toxin-like protein (EC 2.4.2.30) | protein | 176 | 34% helix, 31% strand | W2E3J5 |
| O | Toxin-like protein (EC 2.4.2.30) | protein | 184 | 34% helix, 30% strand | W2E3J5 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, O
- GOL · Glycerol · additive · 2 copies · chains A, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 970 | 0.81 | 0.82 | 92 | empty |
| 2 | 386 | 0.68 | 0.81 | 36 | empty |
| 3 | 180 | 0.63 | 0.84 | 25 | empty |
| 4 | 57 | 0.35 | 0.78 | 15 | empty |
| 5 | 54 | 0.27 | 0.73 | 12 | empty |
Interfaces
1 interface between chains.
- A–O · 963 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5DZQ · C3larvin toxin, an ADP-ribosyltransferase from Paenibacillus larvae, Orthorhombic Form · 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 W2E3J5
- Elsewhere: RCSB PDB 5DZQ · PDBe 5DZQ · UniProt W2E3J5
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