MolNFT v1 · #50368 · protein
Crystal structure of viscum album mistletoe lectin I in native state at 1.95 a resolution, comparison of structure active site conformation in ricin and in viscumin
2RG9 · Beta-galactoside-specific lectin 1 chain a isoform 1: “Crystal structure of viscum album mistletoe lectin I in native state at 1.95 a resolution, comparison of…”. X-ray diffraction, 4 ligands (NAG, AZI, CL), 3 pockets (best…
- PDB
- 2RG9
- 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 isoform 1; Beta-galactoside-specific lectin 1…
- EC
- 3.2.2.22
- UniProt
- P81446
- Ligands
- NAG, AZI, CL, SO4
- Pockets
- 3 · best druggability 0.76
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 isoform 1 (EC 3.2.2.22) | protein | 249 | 37% helix, 28% strand | P81446 |
| B | Beta-galactoside-specific lectin 1 chain B | protein | 263 | 11% helix, 36% strand | P81446 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- AZI · Azide ion · ion · 3 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · 15 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 561 | 0.76 | 0.83 | 81 | AZI, GOL |
| 2 | 87 | 0.43 | 0.79 | 16 | empty |
| 3 | 109 | 0.43 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1477 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 2RG9 · Crystal structure of viscum album mistletoe lectin I in native state at 1.95 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 2RG9 · PDBe 2RG9 · UniProt P81446
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