Research workbench
Galactose-specific seed lectin from dolichos lablab in complex with adenine and galactose
Analyse Galactose-specific seed lectin from dolichos lablab in complex with adenine and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UJO
- Type
- protein
- Length
- 1,006 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Legume lectin
- Ligands
- ADE, GAL, MN, CA
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Legume lectin | protein | 253 | 1% helix, 42% strand | — |
| C, D | Legume lectin | protein | 250 | 3% helix, 46% strand | — |
Ligands and binding sites
- ADE · Adenine · ligand · 4 copies · chains A, C, B, D
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 203 | 0.83 | 0.97 | 44 | ADE |
| 2 | 1038 | 0.82 | 0.84 | 142 | EDO |
| 3 | 110 | 0.79 | 0.98 | 28 | ADE |
| 4 | 114 | 0.77 | 0.96 | 28 | ADE |
| 5 | 54 | 0.69 | 0.97 | 17 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1572 Ų buried · 84 hydrogen bonds · protein-protein
- A–C · 1451 Ų buried · 85 hydrogen bonds · protein-protein
- C–D · 963 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 958 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 136 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 3UJO · Galactose-specific seed lectin from Dolichos lablab in complex with adenine and galactose · 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 3UJO · PDBe 3UJO
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