Research workbench
Structure of the marasmius oreades mushroom lectin (moa) in complex with GALALPHA(1,3)[FUCALPHA(1,2)]GAL and calcium.
Analyse Structure of the marasmius oreades mushroom lectin (moa) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EF2
- Type
- protein
- Length
- 1,168 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Agglutinin
- UniProt
- Q8X123
- Ligands
- GLA, FUC, GAL, CA
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Agglutinin | protein | 292 | 18% helix, 38% strand | Q8X123 |
Ligands and binding sites
- GLA · alpha-D-galactopyranose · sugar · 16 copies · chains A, B, C, D
- FUC · alpha-L-fucopyranose · sugar · 12 copies · chains A, B, C, D
- GAL · beta-D-galactopyranose · sugar · 8 copies · chains A, B, C, D
- CA · Calcium ion · metal · 16 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 895 | 0.77 | 0.80 | 84 | ACT |
| 2 | 295 | 0.64 | 0.80 | 35 | ACT |
| 3 | 262 | 0.51 | 0.75 | 36 | CA |
| 4 | 226 | 0.51 | 0.76 | 34 | CA |
| 5 | 93 | 0.48 | 0.81 | 22 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1509 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 1509 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 404 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 169 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 168 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 3EF2 · Structure of the Marasmius oreades mushroom lectin (MOA) in complex with… · 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
- Every structure of UniProt Q8X123
- Elsewhere: RCSB PDB 3EF2 · PDBe 3EF2 · UniProt Q8X123
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