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Crystal structure of the C-terminal domain of human galectin-4 with lactose
Analyse Crystal structure of the C-terminal domain of human galectin-4 with lactose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CBL
- Type
- protein
- Length
- 542 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galectin-4
- UniProt
- P56470
- Ligands
- BGC, GAL, SO4
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 1% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Galectin-4 | protein | 130 | 0% helix, 55% strand | P56470 |
| B | Galectin-4 | protein | 139 | 2% helix, 53% strand | P56470 |
| C | Galectin-4 | protein | 136 | 0% helix, 52% strand | P56470 |
| D | Galectin-4 | protein | 137 | 2% helix, 54% strand | P56470 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · chains B, D
- GOL · Glycerol · additive · 2 copies · chains B, C
- BME · Beta-mercaptoethanol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 487 | 0.77 | 0.84 | 48 | empty |
| 2 | 101 | 0.37 | 0.75 | 18 | SO4 |
| 3 | 75 | 0.34 | 0.75 | 15 | empty |
| 4 | 88 | 0.33 | 0.74 | 25 | empty |
| 5 | 54 | 0.28 | 0.75 | 14 | empty |
Interfaces
5 interfaces between chains.
- B–D · 817 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 771 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 394 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 372 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 18 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct).
Compared structures
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 5CBL · PDBe 5CBL · UniProt P56470
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