Research workbench
Binding of kinetin in the active site of mistletoe lectin I
Analyse Binding of kinetin in the active site of mistletoe lectin I in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3O5W
- Type
- protein
- Length
- 510 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-galactoside-specific lectin 1 chain a isoform 1; Beta-galactoside-specific lectin 1…
- EC
- 3.2.2.22
- UniProt
- P81446
- Ligands
- H35, NAG, SO4
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-galactoside-specific lectin 1 chain a isoform 1 (EC 3.2.2.22) | protein | 248 | 36% helix, 25% strand | P81446 |
| B | Beta-galactoside-specific lectin 1 chain B (EC 3.2.2.22) | protein | 262 | 13% 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 · 8 copies · chains B, A
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · 8 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 | 414 | 0.76 | 0.86 | 75 | GOL |
| 2 | 231 | 0.60 | 0.80 | 30 | GOL |
| 3 | 111 | 0.54 | 0.83 | 21 | H35 |
| 4 | 124 | 0.47 | 0.78 | 20 | empty |
| 5 | 55 | 0.33 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1441 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 3O5W · Binding of kinetin in the active site of mistletoe lectin I · 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 3O5W · PDBe 3O5W · UniProt P81446
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