Research workbench
Structure of the lectin from platypodium elegans in complex with heptasaccharide
Analyse Structure of the lectin from platypodium elegans in complex with heptasaccharide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZYR
- Type
- protein
- Length
- 481 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lectin
- Ligands
- URE, ASN, NAG, MAN, BMA, MN, CA
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lectin | protein | 240 | 4% helix, 45% strand | — |
| B | Lectin | protein | 241 | 5% helix, 46% strand | — |
Ligands and binding sites
- URE · Urea · ligand · 2 copies · chains A, B
- ASN · Asparagine · ligand
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 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 | 103 | 0.78 | 0.98 | 23 | URE |
| 2 | 93 | 0.77 | 0.98 | 21 | GOL |
| 3 | 71 | 0.37 | 0.77 | 15 | empty |
| 4 | 69 | 0.35 | 0.77 | 16 | GOL |
Interfaces
1 interface between chains.
- A–B · 1092 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3ZYR · Structure of the lectin from Platypodium elegans in complex with heptasaccharide · 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 3ZYR · PDBe 3ZYR
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