Research workbench
Crystal structure mistletoe lectin I from viscum album in complex with kinetin at 2.35 a resolution.
Analyse Crystal structure mistletoe lectin I from viscum album in complex with kinetin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JKX
- 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 a chain; Beta-galactoside-specific lectin 1 B chain
- EC
- 3.2.2.22
- UniProt
- P81446
- Ligands
- H35, NAG, SO4, CL, AZI
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-galactoside-specific lectin 1 a chain (EC 3.2.2.22) | protein | 249 | 39% helix, 28% strand | P81446 |
| B | Beta-galactoside-specific lectin 1 B chain (EC 3.2.2.22) | protein | 263 | 12% helix, 36% strand | P81446 |
Ligands and binding sites
- H35 · N-(furan-2-ylmethyl)-7H-purin-6-amine · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains B, A
- SO4 · Sulfate ion · ion · 5 copies · chains A
- CL · Chloride ion · ion · 2 copies · chains A, B
- AZI · Azide ion · ion · chains A, B
- GOL · Glycerol · additive · 10 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
- DIO · 1,4-diethylene dioxide · additive · chains A
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 | 370 | 0.71 | 0.83 | 70 | EDO |
| 2 | 152 | 0.59 | 0.83 | 28 | H35 |
| 3 | 190 | 0.50 | 0.76 | 28 | GOL, AZI |
| 4 | 97 | 0.40 | 0.77 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1550 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4JKX · Crystal structure Mistletoe Lectin I from Viscum album in complex with kinetin at 2.35 A… · the same entry in another collection · chain A against A, TM-score 1.00
- P81446 · AlphaFold monomer V2.0 prediction for beta-galactoside-specific lectin 1 (P81446) · a predicted model of the same protein · chain B against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P81446
- Elsewhere: RCSB PDB 4JKX · PDBe 4JKX · UniProt P81446
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