MolNFT v1 · #111273 · protein
Crystal structure of the human galectin-4 C-terminal carbohydrate recognition domain in complex with lacto-N-tetraose (lnt)
4YM0: “Crystal structure of the human galectin-4 C-terminal carbohydrate recognition domain in complex with…”. X-ray diffraction, 3 ligands (GAL, NAG, BGC), 3 pockets (best druggability 0.57). MolNFT v1 #111273 on GenesisL1: 3D structure…
- PDB
- 4YM0
- Type
- protein
- Length
- 557 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galectin-4
- UniProt
- P56470
- Ligands
- GAL, NAG, BGC
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 1% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Galectin-4 | protein | 138 | 0% helix, 52% strand | P56470 |
| B | Galectin-4 | protein | 139 | 2% helix, 52% strand | P56470 |
| D, C | Galectin-4 | protein | 140 | 0% helix, 54% strand | P56470 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 6 copies · chains D, A, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains D, A, B
- BGC · beta-D-glucopyranose · sugar · 3 copies · chains A, B, C
- GOL · Glycerol · additive · chains A
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 | 177 | 0.57 | 0.81 | 27 | empty |
| 2 | 75 | 0.47 | 0.83 | 28 | empty |
| 3 | 216 | 0.47 | 0.74 | 25 | GOL |
Interfaces
4 interfaces between chains.
- A–D · 585 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 547 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 271 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 234 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4YM0 · 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 D against A, TM-score 0.98
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 4YM0 · PDBe 4YM0 · UniProt P56470
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