Research workbench
Crystal structure of the tetragonal form of the common edible mushroom (Agaricus bisporus) lectin in complex with T-antigen and N-acetylglucosamine
Analyse Crystal structure of the tetragonal form of the common edible mushroom… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Y2X
- Type
- protein
- Length
- 568 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.36
- Source
- Agaricus bisporus
- Molecule
- lectin
- Ligands
- SER, NGA, GAL, NAG
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · resolution 2.36 · 1 distinct chain · 11% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | lectin | protein | 142 | 11% helix, 53% strand | — |
Ligands and binding sites
- SER · Serine · ligand · 4 copies · chains A, B, C, D
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 384 | 0.86 | 0.94 | 46 | empty |
| 2 | 340 | 0.85 | 0.95 | 41 | empty |
| 3 | 147 | 0.44 | 0.76 | 28 | empty |
| 4 | 141 | 0.43 | 0.76 | 29 | empty |
| 5 | 148 | 0.43 | 0.76 | 21 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1035 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1033 Ų buried · 34 hydrogen bonds · protein-protein
- B–D · 806 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 734 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 220 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1Y2X · Crystal structure of the tetragonal form of the common edible mushroom (agaricus… · 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 1Y2X · PDBe 1Y2X
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