Research workbench
Crystal structure mistletoe lectin I from viscum album in complex with N-acetyl-D-glucosamine at 1.94 a resolution.
Analyse Crystal structure mistletoe lectin I from viscum album in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EB2
- Type
- protein
- Length
- 512 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-galactoside-specific lectin 1 chain a; Beta-galactoside-specific lectin 1 chain B
- EC
- 3.2.2.22
- Ligands
- NAG, SO4, CL, AZI
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-galactoside-specific lectin 1 chain a (EC 3.2.2.22) | protein | 249 | 37% helix, 27% strand | — |
| B | Beta-galactoside-specific lectin 1 chain B | protein | 263 | 12% helix, 37% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A
- CL · Chloride ion · ion · chains A
- AZI · Azide ion · ion · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 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 | 310 | 0.72 | 0.85 | 57 | empty |
| 2 | 179 | 0.50 | 0.77 | 24 | GOL |
| 3 | 127 | 0.49 | 0.79 | 25 | EDO |
| 4 | 113 | 0.45 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1532 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4EB2 · Crystal structure Mistletoe Lectin I from Viscum album in complex with… · 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 4EB2 · PDBe 4EB2
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