MolNFT v1 · #116996 · protein
Crystal structure of the human galectin-4 N-terminal carbohydrate recognition domain in complex with lactose-3'-sulfate
5DUW: “Crystal structure of the human galectin-4 N-terminal carbohydrate recognition domain in complex with…”. X-ray diffraction, 2 ligands (SGA, BGC), 3 pockets (best druggability 0.81). MolNFT v1 #116996 on GenesisL1: 3D structure…
- PDB
- 5DUW
- Type
- protein
- Length
- 551 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galectin-4
- UniProt
- P56470
- Ligands
- SGA, BGC
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 2% helix, 56% 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, D | Galectin-4 | protein | 137 | 2% helix, 55% strand | P56470 |
Ligands and binding sites
- SGA · 3-O-sulfo-beta-D-galactopyranose · ligand · 4 copies · chains A, B, C, D
- BGC · beta-D-glucopyranose · sugar · 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 | 736 | 0.81 | 0.85 | 91 | BGC, SGA |
| 2 | 212 | 0.68 | 0.86 | 35 | SGA |
| 3 | 72 | 0.36 | 0.77 | 15 | empty |
Interfaces
5 interfaces between chains.
- C–D · 501 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 472 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 313 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 263 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 205 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5DUW · Crystal structure of the human galectin-4 N-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 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 5DUW · PDBe 5DUW · UniProt P56470
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