MolNFT v1 · #139426 · protein
Serial femtosecond X-ray structure of agrocybe cylindracea galectin with lactose solved by se-sad using xfel (refined against 60,000 patterns)
5XFD · Galactoside-binding lectin: “Serial femtosecond X-ray structure of agrocybe cylindracea galectin with lactose solved by se-sad using xfel…”. X-ray diffraction, 4 ligands (NDG, GAL, FUC), 1 pocket (best druggability 0.47). MolNFT v1…
- PDB
- 5XFD
- Type
- protein
- Length
- 311 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galactoside-binding lectin
- Ligands
- NDG, GAL, FUC, A2G
- Pockets
- 1 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Galactoside-binding lectin | protein | 160 | 3% helix, 53% strand | — |
| B | Galactoside-binding lectin | protein | 151 | 3% helix, 55% strand | — |
Ligands and binding sites
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 218 | 0.47 | 0.74 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 926 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (engineered).
Compared structures
- 5XFD · Serial femtosecond X-ray structure of Agrocybe cylindracea galectin with lactose solved… · 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 5XFD · PDBe 5XFD
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