Research workbench
Crystal structure of misteltoe lectin I in complex with phloretamide
Analyse Crystal structure of misteltoe lectin I in complex with phloretamide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2R9K
- 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; Beta-galactoside-specific lectin 1 chain B
- UniProt
- P81446
- Ligands
- SGI, NAG, SO4, CL
- 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 | protein | 248 | 38% helix, 25% strand | — |
| B | Beta-galactoside-specific lectin 1 chain B | protein | 262 | 11% helix, 37% strand | P81446 |
Ligands and binding sites
- SGI · 3-(4-hydroxyphenyl)propanamide · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains B, A
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 4 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 361 | 0.76 | 0.86 | 62 | SGI, GOL |
| 2 | 144 | 0.60 | 0.84 | 22 | empty |
| 3 | 147 | 0.49 | 0.78 | 20 | GOL |
| 4 | 157 | 0.48 | 0.77 | 27 | GOL |
| 5 | 88 | 0.45 | 0.80 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1407 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 2R9K · Crystal Structure of Misteltoe Lectin I in Complex with Phloretamide · 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 2R9K · PDBe 2R9K · UniProt P81446
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