Research workbench
Crystal structure of the human galectin-4 N-terminal carbohydrate recognition domain in complex with glycerol
Analyse Crystal structure of the human galectin-4 N-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
- 5DUU
- Type
- protein
- Length
- 552 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galectin-4
- UniProt
- P56470
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 2% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Galectin-4 | protein | 138 | 2% helix, 57% strand | P56470 |
| B | Galectin-4 | protein | 139 | 2% helix, 56% strand | P56470 |
| C | Galectin-4 | protein | 138 | 2% helix, 57% strand | P56470 |
| D | Galectin-4 | protein | 137 | 2% helix, 57% strand | P56470 |
Ligands and binding sites
- GOL · Glycerol · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 726 | 0.81 | 0.85 | 94 | GOL |
| 2 | 249 | 0.71 | 0.86 | 40 | GOL |
| 3 | 52 | 0.31 | 0.77 | 10 | empty |
Interfaces
5 interfaces between chains.
- A–B · 495 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 489 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 276 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 235 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 224 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5DUU · Crystal structure of the human galectin-4 N-terminal carbohydrate recognition domain in… · the same entry in another collection · chain D against D, TM-score 1.00
- P56470 · AlphaFold monomer V2.0 prediction for galectin-4 (P56470) · a predicted model of the same protein · chain A 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 5DUU · PDBe 5DUU · UniProt P56470
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