Research workbench
Winged bean acidic lectin complexed with methyl-alpha-D-galactose (monoclinic form)
Analyse Winged bean acidic lectin complexed with methyl-alpha-D-galactose (monoclinic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1FAY
- Type
- protein
- Length
- 1,888 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acidic lectin
- Ligands
- AMG, NAG, MN, CA
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Acidic lectin | protein | 236 | 3% helix, 45% strand | — |
Ligands and binding sites
- AMG · methyl alpha-D-galactopyranoside · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, C, D, E, F
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1151 | 0.75 | 0.78 | 118 | AMG |
| 2 | 438 | 0.75 | 0.84 | 76 | AMG |
| 3 | 399 | 0.74 | 0.84 | 72 | AMG |
| 4 | 604 | 0.63 | 0.74 | 81 | empty |
| 5 | 343 | 0.59 | 0.77 | 62 | empty |
Interfaces
13 interfaces between chains.
- E–F · 879 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 879 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 867 Ų buried · 4 hydrogen bonds · protein-protein
- G–H · 865 Ų buried · 5 hydrogen bonds · protein-protein
- D–H · 722 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan (N-glycosylation).
Compared structures
- 1FAY · Winged bean acidic lectin complexed with methyl-alpha-D-galactose (monoclinic form) · 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 1FAY · PDBe 1FAY
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