Research workbench
Crystal structure of agrocybe aegerita lectin aal complexed with ganglosides GM1 pentasaccharide
Analyse Crystal structure of agrocybe aegerita lectin aal complexed with ganglosides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3M3Q
- Type
- protein
- Length
- 318 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-tumor lectin
- EC
- 3.1.21.-
- UniProt
- Q6WY08
- Ligands
- GAL, BGC, NGA, SIA
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Anti-tumor lectin (EC 3.1.21.-) | protein | 159 | 5% helix, 52% strand | Q6WY08 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 2 copies
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 2 copies · chains A, B
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 187 | 0.56 | 0.80 | 28 | empty |
| 2 | 58 | 0.35 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 960 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3M3Q · Crystal Structure of Agrocybe aegerita lectin AAL complexed with Ganglosides GM1… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6WY08 · AlphaFold monomer V2.0 prediction for anti-tumor lectin (Q6WY08) · a predicted model of the same protein · chain A 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 Q6WY08
- Elsewhere: RCSB PDB 3M3Q · PDBe 3M3Q · UniProt Q6WY08
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