MolNFT v1 · #28076 · protein
Crystal structure of the orthorhombic form of the common edible mushroom (agaricus bisporus) lectin in complex with T-antigen and N- acetylglucosamine
1Y2W: “Crystal structure of the orthorhombic form of the common edible mushroom (agaricus bisporus) lectin in…”. X-ray diffraction, 4 ligands (SER, NGA, GAL), 2 pockets (best druggability 0.43). MolNFT v1 #28076 on GenesisL1: 3D structure…
- PDB
- 1Y2W
- Type
- protein
- Length
- 284 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lectin
- Ligands
- SER, NGA, GAL, NAG
- Pockets
- 2 · best druggability 0.43
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lectin | protein | 142 | 11% helix, 53% strand | — |
Ligands and binding sites
- SER · Serine · ligand · 2 copies · chains A, B
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 2 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.43 | 0.76 | 20 | empty |
| 2 | 131 | 0.42 | 0.76 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1031 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 1Y2W · Crystal structure of the orthorhombic 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 1Y2W · PDBe 1Y2W
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