MolNFT v1 · #111276 · protein
Crystal structure of the human galectin-4 C-terminal carbohydrate recognition domain in complex with lactose
4YM3: “Crystal structure of the human galectin-4 C-terminal carbohydrate recognition domain in complex with lactose”. X-ray diffraction, 2 ligands (BGC, GAL), 2 pockets (best druggability 0.58). MolNFT v1 #111276 on GenesisL1: 3D…
- PDB
- 4YM3
- 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
- BGC, GAL
- Pockets
- 2 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 3% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Galectin-4 | protein | 139 | 2% helix, 52% strand | P56470 |
| B | Galectin-4 | protein | 138 | 4% helix, 52% strand | P56470 |
| C, D | Galectin-4 | protein | 140 | 2% helix, 52% 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.58 | 0.92 | 22 | empty |
| 2 | 201 | 0.48 | 0.75 | 26 | empty |
Interfaces
4 interfaces between chains.
- A–D · 565 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 541 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 289 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 284 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4YM3 · 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 4YM3 · PDBe 4YM3 · UniProt P56470
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