Research workbench
Crystal structure of the human galectin-4 C-terminal carbohydrate recognition domain in complex with lacto-N-neotetraose (lnnt)
Analyse Crystal structure of the human galectin-4 C-terminal carbohydrate recognition… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YLZ
- Type
- protein
- Length
- 556 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galectin-4
- UniProt
- P56470
- Ligands
- GAL, BGC, NAG, SO4
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Galectin-4 | protein | 138 | 2% helix, 52% strand | P56470 |
| C, D | Galectin-4 | protein | 140 | 2% helix, 52% strand | P56470 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 8 copies · chains A, B, C, D
- BGC · beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 223 | 0.56 | 0.79 | 26 | GOL |
| 2 | 61 | 0.53 | 0.88 | 29 | empty |
| 3 | 64 | 0.25 | 0.71 | 14 | SO4 |
| 4 | 55 | 0.25 | 0.72 | 15 | empty |
Interfaces
5 interfaces between chains.
- A–D · 596 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 547 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 360 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 319 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 11 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4YLZ · Crystal structure of the human galectin-4 C-terminal carbohydrate recognition domain in… · the same entry in another collection · chain A against A, TM-score 1.00
- P56470 · AlphaFold monomer V2.0 prediction for galectin-4 (P56470) · a predicted model of the same protein · chain C 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 P56470
- Elsewhere: RCSB PDB 4YLZ · PDBe 4YLZ · UniProt P56470
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