Research workbench
X-ray structure of the levansucrase from erwinia amylovora
Analyse X-ray structure of the levansucrase from erwinia amylovora in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4D47
- Type
- protein
- Length
- 3,288 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Levansucrase
- EC
- 2.4.1.10
- UniProt
- D4IGH9
- Ligands
- FRU, GLC
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Levansucrase (EC 2.4.1.10) | protein | 411 | 8% helix, 48% strand | D4IGH9 |
Ligands and binding sites
- FRU · beta-D-fructofuranose · sugar · 8 copies · chains A, B, C, D, E, F, G, H
- GLC · alpha-D-glucopyranose · sugar · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 965 | 0.85 | 0.87 | 144 | empty |
| 2 | 859 | 0.78 | 0.81 | 94 | empty |
| 3 | 1174 | 0.78 | 0.80 | 105 | empty |
| 4 | 62 | 0.72 | 0.98 | 18 | empty |
| 5 | 66 | 0.72 | 0.97 | 19 | empty |
Interfaces
16 interfaces between chains.
- E–F · 1151 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1142 Ų buried · 18 hydrogen bonds · protein-protein
- G–H · 1137 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1134 Ų buried · 17 hydrogen bonds · protein-protein
- A–H · 796 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4D47 · X-ray structure of the levansucrase from Erwinia amylovora · 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 D4IGH9
- Elsewhere: RCSB PDB 4D47 · PDBe 4D47 · UniProt D4IGH9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.