Research workbench
Agrocybe cylindracea galectin complexed with 3'-sulfonyl lactose
Analyse Agrocybe cylindracea galectin complexed with 3'-sulfonyl lactose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WW5
- Type
- protein
- Length
- 640 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galectin
- Ligands
- SGA, BGC
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 2% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Galectin | protein | 160 | 2% helix, 53% strand | — |
Ligands and binding sites
- SGA · 3-O-sulfo-beta-D-galactopyranose · ligand · 4 copies · chains A, B, C, D
- BGC · 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
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1071 | 0.72 | 0.76 | 127 | empty |
| 2 | 82 | 0.43 | 0.79 | 16 | empty |
| 3 | 69 | 0.39 | 0.79 | 25 | empty |
Interfaces
4 interfaces between chains.
- B–C · 999 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 998 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 331 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 195 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1WW5 · Agrocybe cylindracea galectin complexed with 3'-sulfonyl lactose · 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 1WW5 · PDBe 1WW5
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