Research workbench
Crystal structure of mistletoe lectin I (ml-I) from viscum album in complex with 4-N-furfurylcytosine at 2.84 a resolution
Analyse Crystal structure of mistletoe lectin I (ml-I) from viscum album in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ELY
- Type
- protein
- Length
- 512 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mistletoe lectin I
- Ligands
- GLY, BFW, NAG, GLA, CL, SO4
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mistletoe lectin I | protein | 249 | 39% helix, 27% strand | — |
| B | Mistletoe lectin I | protein | 263 | 11% helix, 35% strand | — |
Ligands and binding sites
- GLY · Glycine · ligand · 2 copies · chains A, B
- BFW · 4-N-Furfurylcytosine · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains B, A
- GLA · alpha-D-galactopyranose · sugar
- CL · Chloride ion · ion · 8 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A
- GOL · Glycerol · additive · 17 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 301 | 0.77 | 0.89 | 52 | GOL |
| 2 | 204 | 0.55 | 0.79 | 29 | CL, GOL |
| 3 | 108 | 0.55 | 0.84 | 21 | BFW |
| 4 | 98 | 0.43 | 0.78 | 19 | empty |
| 5 | 53 | 0.32 | 0.77 | 13 | GLY |
Interfaces
1 interface between chains.
- A–B · 1514 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6ELY · Crystal Structure of Mistletoe Lectin I (ML-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 6ELY · PDBe 6ELY
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