Research workbench
Agrocybe cylindracea galectin complexed with NEUACA2-3LACTOSE
Analyse Agrocybe cylindracea galectin complexed with NEUACA2-3LACTOSE in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WW4
- Type
- protein
- Length
- 640 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galectin
- Ligands
- SIA, BGC, GAL, GLC, GLA
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Galectin | protein | 160 | 3% helix, 51% strand | — |
Ligands and binding sites
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 4 copies · chains A, B, C, D
- BGC · beta-D-glucopyranose · sugar · 3 copies · chains A, C, D
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains A, C, D
- GLC · alpha-D-glucopyranose · sugar · chains B
- GLA · alpha-D-galactopyranose · sugar · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1045 | 0.72 | 0.76 | 115 | empty |
| 2 | 77 | 0.40 | 0.79 | 24 | empty |
| 3 | 77 | 0.36 | 0.76 | 25 | empty |
| 4 | 68 | 0.25 | 0.71 | 22 | empty |
Interfaces
4 interfaces between chains.
- B–C · 996 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 980 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 357 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 198 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1WW4 · Agrocybe cylindracea galectin complexed with NeuAca2-3lactose · 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 1WW4 · PDBe 1WW4
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