Research workbench
Structure of the lectin from platypodium elegans in complex with a trimannoside
Analyse Structure of the lectin from platypodium elegans in complex with a trimannoside in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZVX
- Type
- protein
- Length
- 483 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lectin
- Ligands
- MAN, MN, CA, SO4
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lectin | protein | 242 | 4% helix, 46% strand | — |
| B | Lectin | protein | 241 | 4% helix, 46% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 74 | 0.76 | 0.99 | 18 | empty |
| 2 | 77 | 0.74 | 0.98 | 21 | empty |
| 3 | 83 | 0.37 | 0.76 | 17 | empty |
| 4 | 82 | 0.36 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1143 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 3ZVX · Structure of the lectin from platypodium elegans in complex with a trimannoside · 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
- Elsewhere: RCSB PDB 3ZVX · PDBe 3ZVX
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.