Research workbench
Crystal structure of agrocybe aegerita lectin aal mutant E66A complexed with P-nitrophenyl thomsen-friedenreich disaccharide
Analyse Crystal structure of agrocybe aegerita lectin aal mutant E66A complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3M3E
- Type
- protein
- Length
- 639 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-tumor lectin
- EC
- 3.1.21.-
- UniProt
- Q6WY08
- Ligands
- NPO, A2G, GAL
- Pockets
- 6 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 3% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Anti-tumor lectin (EC 3.1.21.-) | protein | 159 | 3% helix, 52% strand | Q6WY08 |
| C | Anti-tumor lectin (EC 3.1.21.-) | protein | 161 | 2% helix, 52% strand | Q6WY08 |
| D | Anti-tumor lectin (EC 3.1.21.-) | protein | 160 | 3% helix, 53% strand | Q6WY08 |
Ligands and binding sites
- NPO · P-nitrophenol · ligand · 4 copies
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 327 | 0.64 | 0.80 | 38 | empty |
| 2 | 160 | 0.54 | 0.80 | 29 | empty |
| 3 | 160 | 0.53 | 0.80 | 28 | empty |
| 4 | 129 | 0.50 | 0.80 | 21 | empty |
| 5 | 95 | 0.37 | 0.75 | 26 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1012 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1008 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 455 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 59 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3M3E · Crystal Structure of Agrocybe aegerita lectin AAL mutant E66A complexed with… · the same entry in another collection · chain D against D, 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 3M3E · PDBe 3M3E · UniProt Q6WY08
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